What makes you think he would not? Laver's "on" mode remains unmatched in the open era, so to entertain your hypothetical battle, I do think Laver (who in real history already proved his ability to achieve concentrated dominance) would do what Federer could not--defeat Nadal in a FO final.
Aside from this, I hope you are not operating off of the fact Nadal owned the false GOAT Federer at the FO as some measure of his chances against Laver...
Federer's inability to overcome Nadal has no bearing on someone who already proved he could elevate his game to the ultimate level.
Debating the GOAT no matter what player is favored always ends up a subjective argument. Until Rafa or Nola accumulate the same number of GS titles as Federer then you don't have a leg to stand on.
A google search and Wikipedia about the Rod the Rocket vs Gonzales rivalry? Not really, not even a fair comparison really:
"During the span of seven years that they faced each other, Laver was 26–32 and Gonzales was 36–42 years old. While the peak of Laver was in the late 60s, the peak of Gonzales was in the middle 50s. Gonzales had a great longevity that made possible that this rivalry was competitive. However, the overall record could be biassed in favor of Laver because of the difference of 10 years between them."
In todays game Laver would have been in the top 20, a David Ferrer, a James Blake, possibly a Leyton Hewitt. Laver could maybe would have won one Grand Slam with a little luck two. Otherwise Laver would have been soundly thrashed by most of the top 10 in todays game.
Gonzales at same age would have owned Laver. In fact with his size and athleticism, Gonzales is one of the few players from the by-gone days of tennis that could have dominated in todays tennis, much like Sampras did with serve/volley in todays game.
But, I digress. The evidence I point to for GOAT are the Grand Slam titles and 302 weeks at number one and that is Federer!