I do this for a living. I've already demuxed an Apple-supplied movie with an AC3 track to have a look at it, and I've already tested it on several other players and chipsets I have sitting around the office.
The Apple-supplied movies are legal MPEG-4. They play on anything that supports the profile. The private AC3 stream is quietly ignored. This is the utility of standards like MPEG-4, to ensure interoperability just like this. We're not dealing with crap like AVI and DivX here, we're dealing with a documented standard with specific requirements and known behaviour.
False dichotomy. The two options are not mutually exclusive.
No one is trying to stop you from using MOV containers if you want to. Good luck with that, I hope it goes well.