Nobody questioned Fed's fitness or body fat. Playing that well at the age of 32 tells you something about his physical condition. To be in the GOAT discussion in a physical sport like tennis, you would have to be super fit. It's all relative terms, I guess. Compared to some of the other athletes, I mean. Also the pictures you provided were before back injury. Not so relevant in this discussion anyway. Some of the pictures from KineticChain are interesting though. I still can't believe how the body shape can look so different with little tricks, and I will look into that a bit more to gain some more knowledge on that. If those picture were indeed taken within an hour, all those weight control advertisers should be sued. Very interesting issue to be looked into carefully, I guess.
Anyway, it is silly to question Federer's fitness level. He has not had that many major injury problems considering how long he has been on top level, which is amazing, and to have achieved that, he must have looked after his body really well.