But yep, Apple could do every single thing you say. Without breaking a sweat.
As for why? I think Apple would prefer that OS X not run on commodity PCs. They already take halfassed measures to control running OS X in a VM, and to prevent booting OS X on non-Apple hardware. If they could do that more reliably, they woudln't care about their slightly higher internal costs, and they definitely don't care about making life miserable for their developers (as I've witnessed being one for the past 12 years). But it's just a hard problem for them and a hard sell to existing users used to PCs being wide-open. But with every single iOS user they add, that sell gets one user easier.
I'd bet that within five years, the percentage of users running unapproved software [EDIT: somehow deleted 2nd half of this sentence:] on new Mac hardware will be about the same as it is on iOS today. It won't probably be impossible, just hard enough to not be feasible for most normal/busy people.
OK, that wasn't short, but in summary: The fact that Mac OS X has been the best power user OS for the last several years wasn't by design, it was just an accident of history and where they got their OS from. Apple doesn't give a fuck about power users, and Apple doesn't give a fuck about trucks. That market is just way too small for Apple to care about -- which is sad for those of us currently in that market.
Because if/when Apple finally abandons Intel and power users (timing that makes sense to me) it will be years before Ubuttnu or any other plausible player is anywere near as good as Mac OS X 10.7. 10.8 still has too many bugs and stability issues, but it will get there. Probably 10.9, too. But after that? I don't think anybody knows, but I am very skeptical.
(I think Microsoft will move in this direction, too, so those Surface RT users are probably right to worry.)