That's how good Federer was / has been. Homogenisation helped as well. Djokovic posted similar results in 2012-14 (considering he also met Fedal in two semis) while not being at his best either.
The devil is really in the details - check the number of five-setters played and you'll see. Federer at his peak was one of the best frontrunners who just didn't let it go to five against lesser players, the only exceptions being Haas in AO 06 when Federer was struggling with his ankle and was honestly fortunate to come through and win the title (that's his only major win that actually has some weakness about it based on his patchy play), and Nalbandian in TMC 05 when Federer was visibly hurt and effectively gave away two sets (was actually planning to skip but it would've been an utter disaster since all the other top 5 players - Nadal, Roddick, Hewitt and Agassi - uniquely ended up injured as well, so the orgs convinced him to play with an extra money bonus) - so verifiably not in full fitness on either occasion. The other five-setters were against Agassi (USO 04) and Nadal (Wim 07, Rome 06 for non-slams), two ATGs playing at an appropriately high level.
But come 2008, see who he now plays five sets against: Tipsarevic (AO 08), Andreev (USO 08), Berdych (AO 09, was two sets to love up even). Unbelievable that the tour would suddenly improve so much that an apparently fit Federer (yeah, had mono in AO 08, didn't really tell until the semi tbh, just like Nadal's abdominal injury in USO 09 didn't tell until the semi yet was entirely obvious when it did) would suddenly start playing five-setters against those guys. [Roddick not included, because with some more luck/clutchness he may have well taken Fed to 5 even in 2004, so him playing a tight match against a slightly declined Federer in 2009 was not surprising except for the mental aspect (i.e. having the guts to push Fed all the way, shame about that one volley).]