The point is not that Federer would not be able to hold his own against the clay courters of the 90s, the point is that there were way more than during his time, albeit not a dominating force like Nadal. Kuerten had guys like Rios, Corretja, A. Costa, Muster, Bruguera, Medvedev, Kafelnikov, Agassi and so on and so forth. In 97 he beat Muster, Medvedev, Kafelnikov and Bruguera, a killer draw. This, combined with only 16 seeds, made upsets in earlier rounds way more likely. Of course in a single match, Federer would be favorite against most of these players, but he could very well already face strong clay court specialists in the first or second round, with a little bit of bad luck could face then guys like Kafelnikov, Agassi, Medvedev etc. in the Round 16 or Quarters and finally Bruguera, Ferrero, Muster or whoever in the final. The probability what he would get upset on this road is very high actually.
We can also argue back and forth about hypotheticals. If we start with Nadal, we can also mention (like some in this thread already pointed out correctly), Kuerten's injuries. In the end, without any of these hypotheticals, Kuerten has two FO more than Fed and also straight setted him in their only ever slam match on clay, even though being further away from his prime than Fed. These are straight facts and not some hypotheticals we will never be able to know for sure.