I think he was being honest here. Despite everything that Rafa has done, dominating the clay, winning slams on all surfaces, having numerous winning streaks, being number one in world, winning countless Masters 1000s...he is still the second best player of this era.
Any other era, Rafa would have likely had a few more slams, and been number one in the world for a lot longer. Yet despite everything, Federer is still head and shoulders ahead of everyone in sheer accomplishments.
I mean as good as Rafa's numbers and records are, Roger's are just insane. The undisputed King of Grand Slams, and I'm not just talking about 16 wins, but countless finals and semis to go with it, on all surfaces year in year out.
Of course Rafa will say that despite everything, Roger still won more than I have, and at this point in time, is the better overall player, taking the entire season in. And his real fans would acknowledge that...no point in reason with the ****s.