Wikipedia needs to figure out a way to rectify this discrepancy.I agree with everything you said. And for those H2H nuts out there, they never bother to explain Nadal simply wasn't good enough on HC to meet Fed in countless majors at the USO and AO since 2005. When Fed showed up in those major finals (except AO 2009), Nadal wasn't good enough to be in the final. he was either "injured" or lost in earlier rounds. While Roger made 5 FO finals, thus skewing the H2H even more. He was great enough to meet Nadal in endless clay finals, Nadal was not good enough to meet Fed in major finals on HC's most of the time.
If Fed plays until he's 42, he will almost certainly lose 90%+ of the matches he will ever play again against either Nole or Rafa because of the age differential. Which happens to be another reason H2H's are meaningless.
Seriously, I hope this is highlighted—one way or another—in the history books (or at least becomes common knowledge amongst the hoi polloi).