The RG finals edge is not that big a thing to me. That's more to do with seeding because Novak was #3 or that Nadal was dropped on Djoker's side in 2013 in what was, for all purposes, the de facto final anyway. He played Nadal in the SF's. So basically the only difference was that Federer lost a round later to Nadal.
As it stands, Federer has beaten Djokovic in MC twice, and Djokovic has beaten Federer in Rome twice so that's even. But Djokovic has the versatility of masters titles along with more wins over Nadal at both Rome and MC. The biggest thing Federer has going for him in the event that Djokovic wins RG is that he was the streak snapper in 2011, but as I said, I'd give it to Djokovic if he won RG, but let's not forget that he has yet to do that, and until he does, Federer is the better player on clay.