Roger still has a chance to over Rafa at the end of year
Mathematically, yes, but practically it would be extremely unlikely.
Federer is 344 points down. Winning Madrid, Paris and Shanghai (undefeated), nets him 350 points. Basel and Stockholm would be another 90 (I think).
So with a magic, crazy 2004 Federer style run, he could get 96 ahead before counting any points Nadal earns. Now, Nadal will only play Madrid, Paris and Shanghai, so it is possible that he might not earn 96 points from those three if he's out before semifinals at all three.
But again, practically, one loss will end Fed's hopes, and two or three losses the rest of the year for Fed will mathematically eliminate him, though this cannot happen until Madrid.
I suspect Federer will focus more on preparing for Australia than for reclaiming #1, given his long odds.