Djokovic did manage to win other clay tournaments as you stated in 2011 winning against Nadal in Madrid and Rome, no doubt aided by his winning streak and the confidence he picked up at IW and Miami, while Nadal still won on the slower clay of Monte-Carlo and Barcelona. Other than those 2 tournaments in 2011, Djokovic took 1 more Masters on clay in Rome in 2008. That's it as far as clay titles go, except a couple of minor 250's. I'd hardly call that a record to justify putting him side by side with Nadal on clay unless you arbitrarily isolate history to only count the spring of 2011. Even then, losing to Federer at the biggest clay tournament isn't a plus in his column, no matter his 2 masters wins. We have to ask this question, given a choice, would he have rather beaten Federer to have a chance at beating Nadal in the final at Roland Garros, or be happier with the 2 clay masters?
In that semifinal in RG, Djokovic was very near to Federer playing amazing while Djokovic played great but didn't play great tactically and still made too many unforced errors.
Besides, people keep on repeating about his losses to Kohlschreiber and Melzer at RG while clearly not being in good form, but he also lost 3 times to Nadal in RG, also four times in often great MS finals or semifinals to the same Nadal ...
Besides, I still think Djokovic is very well suited for clay, he was raised on this surface and is more suited to it than Federer.
I'm personally convinced that if he had beaten Federer in that semifinal last year (and he was very near to that, losing two tie-breaks), he would have beaten Nadal in the final. Everything else which happened last year, and the fact that Nadal was not great in RG last year, persuade me for that.