I think the answer to this silly debate lies in whether or not Federer went over his alotted time during the bathroom break. If 2 minutes is the standard changeover time in between sets (if indeed 2 minutes is all he took) then it doesn't matter whether he is taking a ****, wacking off, or sitting on his bench drinking water.
With regard to Nadal, the reason he "happens" to take his T.O.'s when he is down, that is when his adrenaline levels usually drop, thus allowing more pain to be felt. It's a mere physical fact. winning = pain numbed away. Struggling = amplified or returned pain. Nadal is merely responding to his body's natural cues