Every player is different but the 2011 RG semifinal is Federer's best ever performance at RG and one of his best matches on clay period. Anyone who doesn't acknowledge that has an agenda. To somehow parlay that into evidence Federer > Djokovic on clay forever for certain, and old Federer handing peak Djokovic a humiliating loss is purely pathetic, even without what Djokovic is making obvious now at the same age. Also Federer fans like to trumpet him as having the best longevity, but now are making him out to be an old grandpa at the same age Djokovic is still peaking, when Djokovic was more precocious and winning younger than Federer. Isnt that all cute. Sorry this all doesnt work, something has to give.
As for your other point Federer lost to Berdych at the 2004 Olympics, a quite big loss considering he left the court crying despite Federer fans poo pooing the relevance of the event. He only played Berdych on clay and grass in those years other than that, and those surfaces Berdych will never be competitive with Roger (unless he is playing awful like Wimbledon 2010) since he doesn't have the movement or flexability or athleticsm. On hard courts who knows if they played more often, Roger would usually win but I suspect there would be more of a battle. Soderling sucked in those years, of course he wasn't beating Roger or anyone who mattered. If you can beat peak Nadal at RG, you can beat anyone on a given day, as there is nothing tougher in the sport than that.