The FSF and SFLC take the position that the GPL is incompatible with the iOS App Store restrictions, since it forbids adding additional restrictions. However, GPL3 has official support for "additional permissions" and it's still FSF / OSI approved with those added. It permits dropping the additional permissions and using the software as pure GPL3. So that seems like the best approach, but Apple's restrictions are probably a moving target and it would erode the copyleft aspect of the license.
When the author say "we have no problem with you distributing our software through the app store", then I would just get that in some more official writing that include you, apple, and more detailed description on what permission is exactly given. The primary purpose of any software license is to shield the downstream distributor against being charged under copyright infringement, but a personal permission is equally fine in a legal sense so long you don't intend that downstream from you should also be able to distribute your version.
