There's a conflict in distribution, but it's you who cannot distribute them trough this kind of license (unless with the approval of all authors, where the right of *distributing* it is given), you may link GPL programs separately from eg. Aminet, that is if you do not change your distribution terms.
The user is given the right to use said program already, AmiKit to distribute, so if I took those programs from your distro or say, Aminet it's outside of your scope.
