I think when Kabuto said "Prime" he was referring to EMS Madara, that Valley of the End fight specifically. And we know that he didn't have Rinnegan at that point.- And that's why Kabuto completed him to 'beyond his prime'.
By "beyond prime", I'm sure he was referring to Rinnegan + Hashirama's DNA/face/techniques. Though, Madara quickly shot that down by saying that Kabuto didn't give him anything. He awoke Rinnegan by himself.
Kishi can only retcon that statement, because giving Nagato some Uchiha DNA is futile. That's no different from any other Uchiha right? There's no realistic way for Nagato to skip 1 tomoe and go straight to Rinnegan. And in the manga, Kishi establishes that Sharingan-->Rinnegan is unique to Uchiha due their elder son lineage. So Nagato being Uzumaki shouldn't improve his chances of acquiring Rinnegan or grant it to him instantly because they aren't related.- Nagato either; gained Uchiha DNA and not the eyes themselves, awakened it naturally by himself (making Tobi a liar) or Kishi is going to retcon that statement. Kishimoto already confirmed that Tobi and Madara know eachother, so; Madara lived until Kakashi Gaiden (if Tobi is 100% Obito) or Tobi simply isn't Obito in mind or soul.
So that can't work right? Because Nagato had grown up completely by Kakashi Gaiden time, that's a significant amount of time which would make Madara's own statement false - "I died shortly after awakening these eyes"