The App Store is a distribution mechanism, and it imposes restrictions on distribution that the GPL does not have.
One such restriction is that any binary downloaded from the App Store is only licensed for usage by the user downloading it. You are legally forbidden to take that binary and copy it on another iPhone of another user (we aren't talking about technical details and how users could do that, but about what the iTunes App Store EULA says).
Bottom line is that the GPL doesn't allow the extra restrictions that the App Store is adding.
One such restriction is that any binary downloaded from the App Store is only licensed for usage by the user downloading it. You are legally forbidden to take that binary and copy it on another iPhone of another user (we aren't talking about technical details and how users could do that, but about what the iTunes App Store EULA says).
Bottom line is that the GPL doesn't allow the extra restrictions that the App Store is adding.