I don't quite understand this. The GPL gives the end user the rights to the source, to modify the source and to redistribute the software (modified or otherwise), as long as they make the source available. It doesn't say it has to be available through the exact same mechanism that you received the software in the first place, nor does it say that you have to release your changed software through the same mechanism. IANAL, so I definitely could be wrong, but as long as your GPL software links to the code, eg on Github or somewhere, and provides all of the source including your modifications there, any other restrictions the App Store enforces should be irrelevant to the GPL, right? (Unless the app store says you can't link to external source code, or something, of course)
What am I missing?