Seems most on this thread get it.
Federer was never the undisputed GOAT at the time of those loses. Pete had more slams, more Wimbledon titles, more weeks at number one. Federer hadn't even overtaken Sampras, so exactly how was he seen to be the undisputed GOAT exactly? He knew, just like the rest of the world, that the ultimate target was 15 slams, and what would make it even sweeter is winning the RG to give him the edge over Pete. Well guess what? Federer achieved all of that DESPITE Nadal beating him in those previous slam finals. Federer STILL got over the finished line and then set the bar. Nadal only slowed him down and made sure that Federer doesn't look invincible.
IF Federer had FAILED to win the career slam, failed to overtake Pete, then yes, I would say that Nadal prevented Federer from being widely acclaimed as the greatest. It just didn't go down that way though. What you are doing is what most Fed haters do, H2H. Sorry, tennis isn't boxing, it is about winning trophies first and foremost. And while the H2H shows that Federer isn't perfect, his resume still makes many consider him the GOAT and I am saying this as a Djokovic supporter.