This is exactly how iOS works today; in fact Apple recommends you upload your LLVM IR to them and tag your assets as well so they can recompile and recombine your apps for hardware you don't know the existence of yet. Which is nice if you trust Apple…if you don't, then it is very difficult to actually verify that what you're downloading from the App Store is actually what you submitted to the company. With resigning and FairPlay and all the wrappers that Apple applies, it is really difficult to do any sort of verification here :(
Not easily, unfortunately. Accessing the app files itself is usually not possible on a normal iOS device, and even then they are encrypted with FairPlay DRM (which is easy to reverse–but only on a jailbroken device).
I believe the main reason that it was incompatible was a EULA that had incompatible sections and was unwaivable, although those parts are gone now so whether it's still incompatible is not clear.
IANAL and I have no involvement in the Apple ecosystem, so take with a grain of salt:
My understanding is that GPLv3 requires that anyone who gets a binary can also get the source to it, and can then build and run that source on the same device. Even if Apple now allows distribution of software that demands to also share its source code, it's my understanding that you can't build that code and run the result on your iPhone without either rebuilding/reinstalling every 7 days or paying Apple. That certainly seems to be against the intention of the license, although I admit it may technically squeak by the exact requirements.
