I had mine built in 07 I made it part of the deal up front that I was gonna do all the low voltage myself, the builder balked at it for a while saying the similar stuff about how his electrician knows all about automation/theater and if I wanted it I had to have him do it, but when he realized I was serious about this detail making or breaking the deal and I would find another builder he then reluctantly agreed and just said if any inspections failed or held up progress I would be responsible for whatever time/cost it incurred to the job.
Of course I didn't hold up the build at all, his trades held it up as they do on 99% of home builds, I was supposed to close in August, but it wasn't til December before it was done! Typical.
I came in on two different weekends and built sealed speaker enclosures for the inwall / ceiling speakers, preframed for a rackmount, hdmi and ir feeds for all the tv's in the various rooms, ran dual 2" conduits from attic to crawl for up to down low voltage runs later, and 2" conduit from electric panel to attic to add circuits to the bonus room later when I build it out into a entertainment room. Did all the phone, cable, shielded cat6 network , vc's, whole house speakers, ran interface feeds to the doorbell locations and camera wire to the porches, soffits, garage, and driveway.
I met the electricians over time during the build, cools guys but they told me they had no idea what I was doing, and they use crap-ass 18/2 alarm wire for speakers and cat5 for network, they don't do anything else, the customer has to supply the hdmi if they want it or any other cabling etc, and that they HATE doing any of it.
I ran wires everywhere, although I sold the ElanHD w/ Via system I had when I sold the my old house, and I did not have the home automation equipment nor the budget for the near future but having control wires to door bells, v/c locations, camera locations, and access to easily get wires to the attic or crawl and to the electric panels makes it for an easy thing to add in automation and various media devices in the future.
In the end the builder admitted to being impressed, and that he had no clue what I was doing, and he could not have provided any of what I did.
Long story short, the advice is to work out these details BEFORE YOU SIGN THE CONTRACT. Most builders will give in to keep the job, as long as you sound confident and make him understand that you know the local codes to what you can and can't do. (stuff like not drilling through pre-lam beams or pulling wire through the same holes electrical already go through, etc..)
GOOD LUCK on the new house OP, for the future additions you may just need to learn the ART OF FISHING, you can do alot with minimal damage if you really try.
PS to all: CONDUIT is the ONLY thing that is close to futureproof for wiring a new home.