Here is a little diagram I did up. The Red is the bulkhead, the dark blue line is the water line, the grey is the pvc, and the black spots are just the holes in it.
Hope this helps clarrify?
Edit: A bulkhead in the bottom of the tank would need to be plumbed the same way as the one in the lower side, the PVC doesnt really matter on the lower one inside the tank though, you could simply put a strainer to keep macro algae/rock out.
Its in a more accesible position for pods nearer the bottom, and thus I dont think they need the PVC as a 'passageway' to the bulkhead further up the side of the tank.