Congratulations on your plans to build! And having the foresight to pre-wire for distribution, networking, security and automation. All of that adds significant value to your home.
What' you've posted here as a question is actually a long list of questions, decisions and answers. It's a little puzzling that you ask for free advise here when you're clearly sinking a lot of money into building your home. Are you doing all the work yourself? Or are you hiring experts for trades like plumbing, electrical, carpentry, finish trim and drywall? Low voltage wiring is part of a trade too, and there are experts that work in it every day, have the tools and experience to guide you and do the work properly. So, if you're asking here, you're probably doing it all yourself.
Receivers make poor distributed A/V systems. The best ones can handle about 2 and a half zones, but usually with some limits that are hard to understand and barely published. You're mentioning an Atlona 4x4 matrix, but that's still a little vague. There are many ways to distribute A/V these days, some work better than others, but whatever you pick you're going to live with for a long time.
When I come to people's homes to talk about projects like this I have essentially an interview sheet that runs down many questions, very few of them technical in nature, but they help me to discern what the folks value most, what thinks are important, essential, nice to have, not as important, or not wanted at all. I spend quite a bit of time with them, then more time hammering out a solution or three in several cost ranges. You also mention Control4, almost as a given. There are many systems out there, some with significant advantages over Control4. Those of us in the business spend a significant portion of our lives learning about the technology in detail. That's what you pay us for. And what you get is the confidence of using a professional to help you find and install the technology that provides you with best overall value and satisfies your needs, some of which you may not even have thought of yet.
Your post is only scratching the surface, and even if we (I) could give you answers in detail, the would only be opinions not based on your specific situation, so what chance would there be that they'd be worth much?
I don't know where you are, so I'm not offering my own services, but I would highly suggest you bring in an expert to help figure this all out. You might think you're saving money by doing your own work, but what good is it if after all the walls are sealed up you have to rip them open again to put in the right cable? You're "going to school" on your own house, which is fine so long as you know that. Professionals have "gone to school" on many jobs, over many years, and hopefully have actually been to real school too. There's a lot of value in that.