No. I don't think he could beat peak Fed either, and many former great clay courters too. Because of match-up.
Djokovic is a great match-up for Wawrinka because Djokovic is at his best in rhythmic rallies from the baseline, that's when he is the most comfortable. The problem for Djokovic is that this situation it also the one that Wawrinka favors. Stan is at his best when he can hit several relative similar balls in a row, adjust his aim and power, and deliver very powerful shot.
Against peak Nadal, he wouldn't be in this situation because Nadal would apply his usual strategy against one-handed backhand, and it would work, because Stan wouldn't be in comfortable position to deliver his backhand as he can against Nole, and he would make too many errors. It would be the same against peak Fed, who would use all his variety to beat Stan. It is not a coincidence that many of Stan best matches in slams in recent years have been played against Djokovic: AO 2013, USO 2013, AO 2014, AO 2015, RG 2015.
RG 2013 against Nadal is a much better indication of what would happen should they play at their peak than Rome 2015, because Stan was actually playing very well in RG 2013 (he had already had is mental breakthrough against Novak at the AO), while Nadal at Rome was simply an average player.