As I said, it creates doubt. It makes us question the statement. It doesn't necessarilly disprove it, but we shouldn't just take it blindly as the truth, as there are events that can make the statement doubtful.
Madara's rinnegan is another problem. So many OP techs, and why doesn't he use it? Can he use it? Maybe he mastered it in a different way than nagato? I don't really know, so it stays as doubt for the momment.
OT: And besides, it seems that it does come with a manual, The guy gains MS and is instantly able to use amaterasu and tsukuyomi and susanoo. He even knows how to activate it. I've always wondered about the sharingan. Once the user achives it, he is instantly able to use it easily activate it, deactivate it, use the genjutsu, and etc.