What shower fixture is it that you want? Can you post a picture or a link?

https://www.moen.com/products/Moen/Moen_Brushed_gold_ecoperformance_showerhead_handheld_shower/3868EPBG

https://www.moen.com/products/Weymouth/Weymouth_Brushed_Gold_MCORE_3Series_TubShower/UTS33103BG

Linked above - I basically want one tall shower head and one hand held one

You don't need a fixed showerhead if you have a hand held one on a slide bar. I don't click on links on forums, so I don't know what's in your link, but from your description it sounds like a hand held on a slide bar will do the trick, They can do the plumbing like normal, but put the drop ear in a location that you like for the wall elbow (instead of up high for a fixed head). Make sure there is blocking in the wall to attach the slide bar to.

A shower head and a hand held are standard in showers so I don't understand what you would install after. As others have posted, you can find find have a separate shower head or one that is integrated.

In terms of cost, Moen along with Delta are two of the least expensive brands of high quality. I wouldn't install anything lower quality in a shower because repairs or changes in showers are expensive down the line since the rough generally has to be the same brand or compatible with the trim.

I can't offer an opinion as to whether you are being overcharged for the Moon fixtures. Although Moen and Delta are not considered to be high end, the style and finish determines the price. By high end, I am not insulting the quality but just how they position themselves in the consumer market - Brizo is the higher end Delta sister brand.

What does the $3000 cover? When I remodeled the total cost of plumbing fixtures can be shockingly high. My GC or his plumbing tradesperson) supplied the rough and I supplied the trim and told him what the specifications were of the trim so that he could install the correct rough.

My experience is that the shower system is integrated and changing it afterwards is a hassle and expensive. Would you be doing this after the tiles are installed?

The shower components you have chosen are not at all pricey. Have you priced good fixtures (not made of plastic, but with ceramic valves)? $1600 per shower is not bad at all, especially given that Moen makes their fixtures interchangeable, so that the in-wall valves can still be used if you decide you want to change the outer parts for an updated look some years the future.

When doing something as big as buying a house, you will find you have little stomach for more work after moving in and decorating. Why waste the work your builder did and hire someone else (or worse, DIY on the weekends) to redo it? You cannot simply drill new holes and voila! No, your hand-held needs its own water supply and the in-wall valves may also need to be changed to one able to switch to select which of the heads to run.

Think about if you want the slide bar (and water supply) on the side wall (or near a bench) so that you can use it as a body spray, as well. If you do, you need to be sure that the exact placement is specified by you and understood by the builder.