No Britbox, when Federer makes remarks like this it indicates his subservient mentality toward Nadal on clay as well as discrete dismissiveness toward Djokovic. I think any fair-minded person would acknowledge that if Djokovic and Nadal meet at the French this year, given the stakes of the match, it could be a slugfest and Nadal would not go down without a major fight (regardless of the final scoreline). If Federer made a comment to that effect, saying that he expected a tremendous match between two great clay-court players, then I would not have a problem. But for him to emphatically say that Nadal is still the player to beat there, given the current context, is a great indication to me of how much of a wuss Federer has been toward Nadal. It's also an indication of his growing envy of Djokovic.
Let's not forget that Djokovic has ripped two Wimbledons from Federer when he really thought that he was in form to get that 18th Slam and polish off his Wimbledon resume. Let's also not forget that Djokovic has on three occasions, most recently last year, beaten Federer at the US Open in heart-wrenching fashion, twice by holding match points and once by going up against a 98% Federer crowd that made a Davis Cup final seem tame. Djokovic has also been the far better Masters Series player. And, lest we forget, Djokovic has defeated Nadal much more than Federer has, including at the French Open. The ugliest part of Federer's tennis resume is his poor head-to-head with Nadal; Djokovic, on the other hand, has a winning record against Nadal. When you take into consideration all these factors, there is no question in my mind that there is a part of Federer that is resentful and jealous of what Djokovic has done.
I think Djokovic's win over Nadal at the French last year impacted Federer more than most people might realize. Federer never found a way to win two sets on Nadal at the French, and Djokovic straight-setted him. Again, that is another thing Djokovic can say he has done that Federer can't.
As for your defense of Federer, I am not buying it one bit. His only two wins against Nadal on clay came when Nadal was physically not himself. Federer got close on other occasions, particularly in Rome and Hamburg, but for the most part Nadal beat him decisively despite Federer often putting on terrific shot displays in their matches. If you look at their matches closely (e.g. the 2007 and 2011 French finals), you can see that Federer left an immense amount of opportunity on the table by constructing points poorly. Eventually he gave up on the idea of beating Nadal even though it was clearly possible. That is something I find pitiful and that is why I reacted strongly to this latest subtle dig at Djokovic.