It's one thing to make the center console non-standard, it's another to prevent the installation through warranty restrictions.
And I don't know any manufacturer that will sell you someone else's head unit as an aftermarket piece. It's up to you to find out how to take everything apart and fit something else in there on your own, or to find someone who knows—basically, jailbreaking your dashboard. Except you generally lose stuff (like steering wheel controls), while I hear jailbreaking is pretty painless these days.
Edit: Apple's app store isn't some third party stereo store, it's a store owned by the manufacturer itself. And car manufacturers are famous for having highly priced proprietary replacement parts, especially when it comes to electronics like stereos, if you aren't willing to deal with an outside store/brand. I really don't see any way Apple's less flexible with the iPhone than a car manufacturer is with their cars.
Want a custom stereo in your new car with a fancy center stack setup with a non-standard-size stereo and possibly even integrated AC/heater controls? You're going to have to jump through a lot of hoops. Want software with more functionality than Apple exposes to developers? There's always jailbreaking...
In neither case has there been a substantial consumer backlash.