I did put 5/8 plywood on the 2nd floor trusses under a wall. No dry wall cracks in that area. So a little extra beefing up does help. But this leads to the bigger problem you've mentioned and it's even worse for those with a little OC disorder going for them:
Any project that actually got done has flaws, and that is why it got done.
So do what you can, make a priority list of what you want, install in that order. There are also items that can be done after construction, or items where you can do a little bit during construction (like put in conduit) and get it later. Inevitably, later is a few years later, but at least you cat get it.