The rinnengan came from the SO6P, not the uchiha clan. The uchiha's were just the first to figure out how to unlock it, who said no other clan can unlock the rinnengan? Even with that said I don't think nagato was born with nor did he "awaken" his. Just go back to chapter 444 page 17 and read 445, nagato's eyes were transplanted because his rinnengan never turns off. This is why kishi made it so that his hair always covered his eyes. The man talking to obito has to be madara because nagato was minato's age at that time and in a different village. As far as how nagato got those eyes I'm lost but they were def transplanted