I believe that is the case Pulse. In this story they are completely different characters... Maybe....Ah who knows I guess we'll just have to wait and see.
Edit: Just realised that the Prime title doesn't mean they are the leader in this continuity. Look at Sentinel, Longarm and Optimus all of whom bare that name but none are actual leaders of the autobots. Maybe each sub commander has that title. Optimus leading his space bridge crew, Longarm in charge of intel. Maybe RP is in charge of a team of his own?
More food for thought.