Federer being so dominant helps Nadal's numbers in this case. If he'd had less of a stranglehold on the #1 ranking then Nadal might have stolen it a few times in '05-'07. Even though he'd have more weeks at #1 it would be over 3,4,5+ stretches so his "efficiency" would fall.
That is of course true, but he was never close to it. Federer had a really commanding lead throughout. His lead was never below 1500 points, which today corresponds to 3000 points - a Slam and a Masters. If there should have been back-and-forth then 2008-10 would have been the time for it.