1) That what you wrote shows consistency, only. 2) That Federer being more consistent doesn't mean that he's better than Rafa. 2) You using the "he got further, so he would've won if they played" argument is deeply flawed, especially when it comes to Rafa, and his injuries.
The thread title is provocative, but I think the analysis therein is interesting and thought-provoking.
Tennis fans, unless they have an agenda, would usually agree anyway that H2H is not a very meaningful metric, given the issue of match-ups. It is also well-known that the Federer-Nadal h2h is strongly skewed by playing on clay, where Nadal is and has been undoubtedly the better player.
What
@falstaff78 shows here is something more nuanced, which is that, even beyond the clay-versus-not distinction, when you look at tournaments / parts of the season where traditionally Nadal has done well, his h2h is ahead there, whereas when you look at those where Federer tends to play better, he has the better h2h. The former happened more frequently than the latter (due to Fed's greater consistency across the years on all surfaces / Nadal having more injuries / whatever), and this skews the H2H strongly in favour of Nadal.
Now, of course
@falstaff78 hasn't done a proper statistical analysis (and we couldn't expect them to), the data is by nature somewhat limited, and speculating on what would have happened if Nadal had made more of those matches doesn't give anything conclusive. However, the data is pretty compelling, and moreover turning the question around, it is fairly indisputable that, if Roger had had similar overall results on Nadal's turf as Nadal had on his, then his h2h would look better even though his results overall would have been worse.
I don't think the numbers argue whether Fed or Nadal is better; after all, I think they show that their record is pretty even against each other when these factors are taken out. However, it does challenge the conventional wisdom of how big Nadal's match-up advantage has been against Federer.
I speak as a Federer fan, but trying to keep all my biases away as much as I can, I don't see how anyone neutral could dispute that Federer has been the better player over his career so far than Nadal. (Of course, neither of them is finished, and Nadal is 5 years younger, so this could well still change - we'll see.) They are both amazing players, and have had amazing achievements, and have had amazing highs (as well as some lows). The only question is whether, if their other achievements get close, the H2H should play a role in determining who is greater. These stats go some further way to convincing me that it shouldn't (one way or the other).