The dialog lists Alt, Ctrl, Hyper, Super as modifiers, which is slightly confusing, since both Hyper and Super are mapped to mod4 in our default modifier mapping, so selecting either has the same effect. It would be better to either *) Remove the Hyper choice from the dialog or *) Map Hyper to a different modifier (mod3 is currently free)
A good fix would be to only show those in the dialog if they're bound: We can call gdk_keymap_get_entries_for_keycode() to check if either are there, and show them in those instances.