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.
