did they offer any energy efficient upgrades? Or I should ask, where is the home located and what is the exterior shell construction like? Energy efficient upgrades and air sealing enhancements should be your FIRST place to spend money. It is the only place in your home to have any sort of a pay back for you. What windows are they including?
As for the rest of your list, its really impossible to have any idea on costs associated with the house with seeing a plan or knowing sizes of spaces.
For example, the wood flooring. If your home is 4k sqft, thats a great price. If its 1k, thats a really bad price. However just looking at the prices, nothing is really jumping out at me as way higher then it should be.
I would probably not have the builder responsible for appliances. I would think that is an area you would like to have complete control on what you select.
No one here can really tell you which one of those cosmetic items you should or shouldnt do since it is your home. Do it how you like it!
Typically the more you can compile into the build process, the better. It MAY be possible to do it afterwards, but also consider the mess and additional time it will take to fully complete the house. Discuss with him owner-provided items and ask for install only pricing too. Sometimes they are flexible with this and give you a good install price. Just know things like this are up to you to have things ordered, on site and correct to meet the timelines. If things are delayed, they come at a cost, which is out of your pocket not his.

Thank you for your reply! I had so much on my mind that I neglected to mention the square footage: 2,500 sqft. Yes, the house is energy efficient....our builder is known to be a "100% energy star builder" here in the Pacific NW.

please elaborate on "energy efficient". Is he applying exterior foam to the (assumed) 2x6 walls? Are you blowing your insulation (fiberglass, cellulose or foam) instead of fiberglass batts? Is he supplying an air tight package that included caulking and sealing with blower door testings and a HERS score/rating? Will it really be an energy star home, and if not, is he building per Energy Star 3.0 guidelines still? Also ES 3.0 is a good base point, but why not go above and beyond slightly? You are looking at spending $15-20k+ on cosmetic enhancements. Why not just spend a few more k on exterior envelope improvements and have an even higher performing, lower utility bill house?
Just some food for thought. No one ever wants to spend money on things they can not see, even if it saves them money and gives you a more comfortable, healthier home.

Here is a little more of what they include in being energy efficient:

R49 attic insulation

Energy-efficient 96% Bryant furnace

Duct Blaster test performed to check air sealing of duct work

Low-E vinyl spectrally selective glass windows, which reduce heat and UV rays

80% fluorescent lights � interior and exterior

Blower Door test performed to check air sealing of house

Advanced programmable thermostat with multiple time and temperature settings

ENERGY STAR� Dishwasher

Energy efficient water heater

** I don't know if this means anything but their HERS rating was 65 and they compared it to a typical energy efficient NW home to be at 80 and many new construction homes to be at 95 (the lower the score the more energy efficient)

These are just the "included" features...there is the option of a tankless water heater as well but we are unsure if we will be living in the house for more than 5-6 years, so thats still up for debate.

that is a good starting point. what about your exterior walls?
tankless waterheaters are not nearly as efficient as they attempt to sell you on.
Curious question however, why build and only be there 5 years?

My husband is in the military...ideally, I would prefer to build once and have it be our forever home but we don't always know where we will be but since my husband will be retiring in 6 years, we will have the option of staying here or moving back to the east coast. We found it is a far better investment to build than to buy used (mainly resale value, esp if we decide to sell in 6 years or so).