To be fair Federer has avoided playing Nadal on clay in the past two season. The head to head could have been more in Nadals favour.
That's a hypothetical thought experiment that could also never happen. Fed could've been bounced in the earlier rounds and never faced Rafa.
With only Thiem and Zverev seen as the main threats to Nadal on clay. I’m sure Federer would have met Nadal a few times on clay in the past 2 seasons due to the lack of competition Nadal has on the surface.
I’m not sure what age has to do with it though. When both were at their peak the rivalry was massively in Nadals favour and even the most hardest of Fed fans would admit that.
You could argue with Djokovics head to head against Federer. Djokovic beat Federer a lot of times when Djokovic was at his peak and Fed was past his best. Whilst Federer was beating Djokovic early on in the rivalry when Djokovic was still clearly raw. So that rivalry head to head you can say isn’t really accurate as there was never really a time consistently when both met at their peaks.
Where as Nadal and Fed both met each other a lot of times at their best. The matches most of the time went in Nadals favour.
The point is head to heads are just one of many more factors that can be evaluated - such as most singles titles, most weeks at #1, most consecutive weeks at #1 etc. These are all important facets to evaluating the entirely of a player's career.