Apple also owns the app store and the default configuration of the OS is moving towards only allowing app store software (has it already finished that transition)?
They can and will reject anyone who uses private apis that they themselves use.
In addition, because they own the OS they can require that a private API is only accessed by software signed by them.
It also could cause firefox to break on OS updates and would require firefox to keep abrest of those changes.
You can still install any software you want on your Mac. As that bugzilla page says, Firefox already uses plenty of private APIs, so this doesn't seem to be a big deal in practice. And Firefox was not rejected from the App Store, another XUL client was (IMVU).