I can't really see where Federer really should've taken advantage. The whole point being made is that typically Federer would take care of an ATG in their infancy but didn't because of the match-up, which in early days we could see plain as day even on HC. There's nothing more beyond it than that. It isn't about his record and all matches up till 2008 Wimbledon. It's about something else entirely - the curious case of the Fedal match-up as evidenced even in its infancy with a not yet fully matured Nadal. There's no angle suggesting that Federer should've taken advantage (or more advantage than he did).Federer only lost 2 matches to Nadal outside of clay until 2008 Wimbledon.
3 matches until 2009 AO.
4 matches until 2011 Miami.
I can't really see where Federer really should've taken advantage. Even if he won all the matches on HC/grass during the time he would still be like 15-20 behind in the h2h. The problem was Nadal not getting to Federer than Federer losing to him outside of clay.