I have apper and gnome-packagekit on my system, the latter from groupinstall KDE for occasional testing there.
virt-manager calls out to packagekit on first run. I was just testing it out, while logged into gnome, and apper popped up rather than gnome-packagekit. I don't know what package decides what UI to run but I figured I'd start here.
This is up to date Fedora 20.
both gnome-packagekit and apper provide the same dbus service, but afaik, there's still no way to prefer one over the other, see dbus bug #484945
*** This bug has been marked as a duplicate of bug 484945 ***