Pretty much what everyone else says. Madara transplanted his eyes into Nagato, Obito however later stole both eyes from Nagato's corpse. Obito only used one rinnegan eye in the battle and the other rinnegan eye was hidden.
I believe if Naruto had the fact still about Kamui then Sasuke would be weaker against Naruto with BSM. But if Naruto did not know that then I believe that Kamui Sasuke would defiantly be a bigger treat against Naruto.
But when you say that Sasuke have Kamui, will he still have Susanoo'?
I believe that Naruto can take this yes. By combining KM/BM (whatever) and SM then they are pretty much doomed. Sage mode allows him to sense their attacks before they do it, and KM grants him the speed. Also apparently nothing can penetrate his chakra skin anyway.
And I do believe that he can...
I don't want any of that to happen anyway, if any then Naruhina. Still I find it weird that Naruto suddenly became the most successful man in the whole planet.
Even Obito gives Naruto tons of chances to make him understand his feelings, his despair, his pain. Still Naruto keep rejecting but...