No the right side case won't fit on with the Rotopax there. That would be where the top positions come into play.
The side position is more designed for a "fast and light" setup where you run a top roll bag or a Giant Loop Great Basin bag or some thing like that. You could probably also run a Wolfman Alfa/Beta with the Rotopax turned horizontal but I have tried that...yet.
There are so many options I still have to figure them all out...