The surface doesn't effect his mental state, and he has choked against Nadal a lot before, he'll be ahead then play a bad point and lose it and start coming in at the wrong time, or dump a 2nd serve into the net on breakpoint. He only needs Nadal to break him (one bad service game) and it could happen. It might not, but it could. I mean Federer had never choked a match away to nadal on grass until 2008...fisrt time for everything (EDIT he didn't choke the match away but he choked in it, everytime he got break point).
In 2006 and 2006 he was both a better player and he had wins at Wimbledon he was coming off (in terms of last meetings with Nadal) and that 2007 win brought the H2H to 8-6 in Federer's favour, so really he was not getting beaten by Nadal almost every time - he had much less mental scars against the guy. Last year he played very well and his backhand was a weapon, but that doesn't mean it will be like this every match.
I'm surprised that people can say Nadal is such a big underdog on the basis of 3 matches over 5 years. It's just a sea of overconfident Federer fans and Nadal fans making him super underdog so that when the inevitable happens and Nadal does beat Federer at the WTF at last (maybe not this year, but some year in the future), it will be hailed as a monumental feat, when in reality against a 30 year old Federer it's probably 50/50 at worst. I mean if they had met 6 or 7 times indoor and Federer had won every one, fair enough although age still catches up with you. But 3 meetings? Not a lot to base the belief that even an older Federer has it in the bag.
Do't get me wrong, I think Federer playing well and not choking would win 9 times out of 10 indoors, but I can't rely on both those things happening. I mean I think a Federer playing his best would have the edge on most hardcourt and grass just like Nadal would be virtually unbeatable on clay, but the H2H hasn't worked out like that