Because ones a team sport and the other ones individual? Most reasonable people understand that in a team sport, there is only so much influence an individual can have. So punishing Maradona for the collective failures of an organisation is just stupid.
Not to say it doesn't happen. Look at the LeBron James Vs Michael Jordan debate.
Thus the question still remains: why is Maradona considered the greatest, or one of the two or three greatest, footballers of all time? Clearly, it's not the stats; so again why do we "feel" that he is so?
And btw, Nadal's H2H is better against Roger because they met way more on clay than any other surface in the early period. That's no excuse for Federer and it shouldn't take anything from Rafa, but when this is a result of Federer repeatedly making it to the finals on clay , while Nadal failing to reach finals as frequently as Federer on hard and grass, then it clearly shows that at least the calculation needs to be more nuanced than simply counting the H2H matches.
This is the other problem I have with the simplistic model of counting GS, or world cups in football, to determine GOATs. They do not show the full picture. Why do ATP finals, where you compete against the top 8 players of the year, not count in a GOAT debate? At least give it a lesser weight. Roger has 6 of these, Nadal has 0! What about Masters 1000 or 500? The model needs to be way more rigorous.