Yes, they won't support dual booting linux - you can run a VM, but if that's a dealbreaker - fair enough.
There's absolutely no chance however that savvy users will not be able to continue running non app store apps.
Apple want control, but they're not stupid enough to completely lock down the development machines for their entire ecosystem.
There isn't much people can do about that though? You basically have to run their OS to develop apps for Apple products, and people who don't develop apps for Apple products don't use Mac's anyway. Just make a laptop appstore with everything you need to develop Apple products and they could force all programs to go on it and they would lose almost no users of their laptops.