Truth is we do not know when the SO6P got the Rinnegan, was it before or after he sealed the Juubi within him? Knowing this will either give us the answers we are looking for OR generate more questions...a lot more questions.
If it was before then this raises serious questions as to how it occurred and mutated into the Rinnegan. Plus the other question would be, how does the Juubi's eye fit into all that?
If it was after then it makes perfect sense considering both the Byakugan and Sharingan are mutations of the Rinnegan based on what was told to us by Obito about the Elder son.