That is easy to illustrate. Look what happens in this years AO and Wimbledon. In these two tournaments Fed gets a W and an SF, giving him 2720 points. Nadal gets an F and a 2nd round. That gives him 1245 points, less than half of Federers total. But he also has 1-0 H2H against Fed separately in these two tournaments - beating him in AO. So you see, H2H against individual players does not explain rankings. But I don't think EMB will take this argument, as it does nothing to help his case.....
An interesting point is that if Nadal had reached the semi-final and lost to Murray at Wimbledon his head to head versus top 4 players would be worse this year, but his GS performances would have been much better (F, W and SF instead of F, W, 2nd round and his top 4 would be 2-2 instead of 2-1).
Tennis is about the whole draw not just the top 4 players.
Doing well against top 4 is great, but Nadal has also had far more "bad" defeats than Federer i.e. players such as Rosol.