I can't with your decisions except to say why would you want to have to find tradespeople to do all these little items after the build is completed??

No comments on the rest but the shower niche should be built as a part of the shower and waterproofing.

I have no idea about 1/2 of this stuff being up charged . The pot lights I think I need to know where you want them The fans all bedrooms have electrical in the ceiling for a light so if that is the case take the cheap bulders light and change it to fan later . IMO you never choose the backsplash until the whole kitchen is in so do it DIY later I hate shower niches so that for me would be a no.. Yes to charger in the garage .Electrical outlets not sure do you have real high need for more ? I hate these kind of builders that every tiny thing is an upgrade. Yes you can add dimmers anytime just make sure the bulbs work with the dimmer.Definately do not need a humidifier where you live.

"Shower niche - $600 - this sounds awfully expensive, is it possible to get this done later for cheaper? Wife is adamant she wants this."

This must be done when the shower system is being designed, built and waterproofed. It cannot be added later without destroying the waterproofing and retiling a good portion of the wall. Most of the other things are easy to DIY if you have skills but you need to decide what your time is worth. Since you are asking here it sounds like you would not be doing it DIY. But If you will be hiring out, cheaper, cleaner and neater to do it now.

Our local code only requires 1 regular outlet per vehicle in the garage (not including the one on the ceiling for the garage door opener). I'd pay for more in the garage in a heart beat.

It might not seem cheap but any of that stuff is compared to putting it in later. The one caveat being the USB plugs. They cost about $40 if you can change them yourself.

Edit to add - oh and the back splash. I would also do that later or have them put in a 2" or 6" one matching the counter top. If you do it later make sure they don't install a 4" one. And if you can, and have a window sill in the kitchen, see if you can have it the same material as your counter tops. I love mine.

HVAC humidifier -- if you will have forced air heating, air will be very dry in the winter. A humidifier may make it more comfortable.

220V outlet in garage - definitely!

Kitchen backsplash - do later but do not have them install a 4-in backsplash

Recessed light 4" -- I definitely wouldn't want to have 8" and obviously, you would have to patch the ceiling if you change to 4" later -- probably why they priced it $175 each because most people would want to pay this additional charge now instead of doing it later and so a good money-maker for them

Wire and install flush mount ceiling light - $225 -- what does this mean? Not doing this means there will be nothing there? If you want a ceiling light later, would you have to get electrical wiring there. You need to decide if you will want to do this later - if so, I would be fine paying an additional $225

Wire and install buyer supplied ceiling light - $175 What does this mean? Not doing this means there will be no wiring there?

Keypads, additional USB outlet, etc.-- these are little items that together really don't seem to be much relative to the whole cost of the house. If getting a mortgage, these wouldn't really make any difference on your monthly payments so I would do these now

Get everything you need that runs inside the walls and things that will make a big mess and cost a lot more if it's done later.

I would just get the wires for the ceiling fans installed and pick out your ceiling fans yourself.  I bought Hunter Fans and am definitely pleased with the quality and silent running.  Your builder will install cheap builder grade fans and is marking up the price.  You can install dimmer switches yourself. Make certain the electrical switches and outlets are enough for each room.  Do you need a floor outlet in the living room?   Where are the two outdoor faucets located…ie near the driveway and front yard and backyard?  Are they weatherproofed?

Pay for the shower niche…you cannot add that later.

Get the under cabinet lighting installation hard wired.   The under cabinet lighting should be installed farthest from the wall.  

Make certain you decide on LED lights color spectrum for ceiling light and cabinet lighting and keep it consistent.  2700 K is warm, similar to incandescent bulbs. 3000K can be rather sterile looking, in my view.  Any higher Kelvin is harsh.   I use 2700K 60 W equivalents in my mini-chandelier and pot lights , and chandelier in dining area.  I have a dimmer for the dining area. 

Don't get the backsplash from the builder, but pick out a backsplash you love and do it all the way up to the cabinets, unless you can get a quiet counter top and matching solid  backsplash that will go up to the cabinets. 

Get what you love and do it right.  Enjoy your new home.

A car charger is a specialized piece of equipment. I would not have your builder charge you $650 for an outlet you likely will not use for charging. If you want to find out about chargers here's a YouTube channel dedicated to comparing your options. State of Charge . .An outlet doesn't include the cable of the length you need. This can depend on the location of the charging port on your car. I have a Tesla. I charge it off a 120v outdoor outlet overnight. If I wanted 220v a Tesla will take a 2 wire + ground 220v 50A NEMA 6-50R outlet. Industrial grade is $35 for a Bryant. Two wire line is less expensive for the run from the fuse box and the run from the outlet. No need for a 3 wire + ground 14-50R.

If you do decide to get this expensive overpriced outlet, insist on an industrial grade receptacle. Charging takes hours of high-power flow. A standard dryer or range type receptacle will overheat, burn up and fail. You must use the thicker, heavier industrial grade. Bryant is good. Made by Hubbel. Ask for the box for proof.

Humidifier. Lots of people think that forced air hear dries out a house. They are wrong. What dries out a house is air infiltration. Yes - a forced air system designed poorly can lead to increased air infiltration. A new house would not be like an old house in this regard --- hopefully. I have no humdifier in this house and forced air heat and no issues at all. I lived in a rental new townhouse and it was shocking... because it was dry. There was a terrible amount of air infiltration.

Air filtration is an extra air filter that you don't really need. Does a better job than the crap intake filters but whether you would notice would depend on lots of factors. My house is so lacking in dust that it takes like a year before I can see a subtle change on the intake filters (return is the proper term but is a bit confusing). I really don't know why this is but I credit a lack of air infiltration.

The garage outlet wiring charge really depends on where the breaker box is. If it is in the garage, it is such a ripoff that I wouldn't do it on principle. And later would be close to same cost. And you don't know where the outlet is on the car. Fun story - I knew but we changed cars and the preferred location changed 2 months after we moved in. Sure - the cables are long enough that it doesn't matter that much. Most of the time...

You know - you have so many electrical wants/needs, that I would consider the design of the house and the feasibility of retrofit. Since most of your issues are electrical, it would be a single contractor (and perhaps a drywall repair person - but I am talking fully accessible). Recessed light on a ranch house with a sealed attic is pretty easy later. Ditto the ceiling fan. You might be talking $5k in options that you could do for a small savings later.

Niche is a no brainer as mentioned. Backsplash is also a no brainer to not do.

It's up to you to decide how much money now or DIY/hire out (which for some options can be done over time) you can handle. Just to expound on each item, as it seems like you are a bit "green" to this process:

- 4" recessed lights: It is much less $ to install now, easier to run wiring, locate switches, and your fixtures will match. Depending, it could change your circuit layout. But you will need to mark up a floor plan for which rooms and determine exactly where and how many more than the eight already provided (wherever those eight are). If you swap from already provided ceiling mount lights, clarify if you get some credit for those.

- Ceiling fan install: If you want separate light and fan control, that will require an extra wire and possibly a larger switch gang box, presumably beyond the already provided generic ceiling light in the middle of the room. Also would be good to use a ceiling fan box which is more stable than a standard box. So much less $ to install now. You can clarify 2 switches or a more expensive single unit light/speed control. The other option is not worry about any of this wiring by using a remote control, but that has obvious drawbacks.

- Standard electrical outlet: This is for those beyond what is shown on your plan, which is certainly only minimum code. So if you want a high-mount tv, a lamp in the middle of the Great Room, toilet seat bidet, Xmas lights to plug in at the soffit or on a future pergola, behind both nightstands in the Master, etc. now is the time to do them. Will require scrutinizing of the electrical plan. There may be additional beyond the $150 for floor, waterproof, soffit, or GFCI receptacles.

- Non-recessed ceiling lights (builder or buyer provided): Again, scrutinize the electrical plan to see what is already being provided and where. In most cases, it is faster and cheaper to go with any lights a builder provides, then at some future point you can change out a fixture to your taste.

- Undercabinet lighting: Much easier to install now. However, there would be a lot to be clarified by both the builder and you. You can direct wire a bulky fixture, or provide an outlet hidden somewhere to hide a slim fixture's transformer, and have them on a switch or not. And, there is a method to how you light a kitchen, so a generic 36" may not meet your expectations. Evaluate this in relation to whether this is a "value-oriented" tract house, the kitchen layout, and your cooking needs.

- Dimmers: Not much to swapping a switch later. No different than changing a ceiling mounted light.

- Keypad: Only requires some button programming, directions are included.

- USB: Same ease as swapping switches to dimmers. However, you may have certain locations that would be hurt by eliminating a "plug" on a duplex receptacle. But, there are a handful of options, some with combo "plug"/USB, only USB, duplex "plugs"/USB, and some with all different USB/speaker/etc. Because the $140 cost is near the $150 for a regular receptacle, clarify that this would be adding an additional receptacle next to an already provided receptacle. That might be advantageous in certain areas like the kitchen drop zone or Master nightstand. Again, scrutinize the electrical plan.

- Car charger: This is only bringing the circuit to the garage, not the actual EVSE unit. A 50A/240V providing Level 2 charging is the best reasonable future-proof you can do now, and $650 is probably 1/3-1/4 the cost to do it later. Clarify that the builder is providing a receptacle at all or just a junction box, and a 14-50 receptacle is most flexible and best for all unknown scenarios, but will require more wire.

- Niche: Must be done at time of rest of shower. Happy wife, happy life.

- Backsplash: A set price means a set product line and simple design layout, probably no detailing like behind stove or crown. Verify what it entails and see if it matches your expectations. It is simple to do later.

- Humidifier: If you have a value-oriented tract house with a single-stage furnace and no room returns, it may be best to keep things simple and not worry about humidity control. A more complicated and exact system (e.g zones, complete returns, cfm balancing) may want some control and the cost associated with that.

- Air filter: Assume that is for electronic air filter. Same as humidifier, evaluate bells and whistles.

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Note that these just address your builder options. There is a whole world of opportunity you could do, of course each with a price tag, but it sounds like this is a tract home build and you are only given a menu. The next house build you will know exactly what you want.

3 onthetree beat me to it. If you know you want ceiling fans in the bedroom, let them install the far superior ceiling fan boxes now. Please don't just add the weight of a ceiling fan onto a standard light box. Bad things can happen. At a minimum it's hard to keep the fan from wobbling, at the worst the light box won't support the weight of the fan and it comes crashing down....

what 3onthetree said is great.

My only exception would be the USB outlets. Everything is forever changing. My phone right now doesn't have an end that goes into a USB, so it's another piece I would have to get. Much easier to just plug it in with the adapter.

I do find that during the cold winters and having a wood burning stove and electric heat, I run a humidifier alot. Think about that one.

I would also add - a plug for a generator so you can just plug it in and throw the switch when power goes out.

Congrats on the new house! Good luck

Thinking about what Debbi said on the USB, here is a small selection of different plug styles, there's probably 30 more variations:

Some are combo electric+USB, some dedicated. So that would be part of clarifying if the builder provides a combo or a separate gang box. The dedicated would be better because the combos get pretty tight with cords. In the future, if you aren't keen on a drawer full of different adapters from Amazon, you can switch out the type of USB as simple as a dimmer or ceiling mount light does for around $15-$20 (about the same as some Apple certified adapters - it's a racket). You can see just recently a lot of electronics are moving from USB-A to USB-C.