Fed would have still been a great player.. But not nearly as consistent (since he would have had to keep his 2003-prior style) and with that comes way more inconsistency, He wouldn't be able to play the safe baseline style in the 90s. He would have had to go for broke much more. Chip and Charge a lot more etc.
He would have had more threats to contend with around ALL SURFACES than he did from 04-07. His resume is pretty over-inflated because of his domination of a weak transitional era of 2003-2007.
Hes would be great but just not nearly as great as he was in the 00's is all.
The 90s would have been like the 80s in essence. Lots of great players (that could have had GOAT-like resumes if they played in a transitional weaker era like Federer did from 2003-2007. Pre Nadal, Djoker and Post Sampras-Agassi) but all of them taking slams from each other (Sampras, Agassi, Courier, Federer, etc.)