definitely the south side. If you do a custom rail that doesn't have a 1st waypoint, then you don't need to worry about where you need to put your rune location. The basic rail has a waypoint outside (and right to the south of the gate), so that's why you are required to have your rune to the south. Actually, the other rail I posted doesn't have that 1st waypoint, so that rail works N,S,E and W.