The App Store's incompatibility is by Apple Policy, enforced via digital restrictions management. See the license says that after Apple distributes it to you,

The App Store's incompatibility is by Apple Policy, enforced via digital restrictions management. See the license says that after Apple distributes it to you, they have to permit you to change out libraries and code and still have it be runnable. As this would permit you to run custom code on the iDevice without Apple strictly controlling what computing you are permitted to perform on an iDevice, Apple cannot allow this. So Apple bans GPLv3, because they do not permit you to do what you want with your device, the device does what Apple wants and permits you to do with it.