I'm not learned on the anatomy of marsupials. However, the first thing I thought of was: Why is upward or downward assumed to be the original orientation? My initial suspicion is that inward was the original orientation, similarly to a uterus. Rather than the opening of the pouch moving I would suspect that the base of the pouch moved from the inward apex to downward for the kangaroo and upward for the wombat. This would give us the current illusion of a downward opening when in fact it was the pouch itself that moved, not the opening.
With this series of events, small incremental changes from the inward pouch apex would have been beneficial for both the wombat and the kangaroo in their respective directions.
I guess its a bit hard to explain without diagrams.