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That's a common misconception. As far as we know the Rinnegan is not an evolution of the Sharingan but rather the Sharingan that is a degeneration or dilution of the Rinnegan. Most theories also blame a cross breed between the Rinnegan and the Jubbi's chakra.
With that being said just because you mastered the black belt on Karate that does not mean a white belt can't land you a blow on your face. Mastering something does not grant you immunity to it, especially since Nagato never had the Sharingan and therefore does not know their techniques nor how the work.
If we were talking about Madara then I could assume that this logic might work but not with Nagato.
Dammit. I was just about to say something like this. >__>