Yes. Djokovic's style has always been a tough matchup for Nadal, but Nadal could always overcome it and win through persistence, fitness and determination if Djokovic went toe-to-toe him in a match before 2011. I'm talking here about their matches like 2008 Hamburg, 2008 Queen's Club, 2008 Beijing Olympics, 2009 Monte Carlo, 2009 Rome and 2009 Madrid. Djokovic would ultimately be grinded down by Nadal's determination and physical game. The situation since 2011 is very different because Djokovic now has a lot more stamina and is very rarely out of position on court. Because of this, he dictates the rallies against Nadal with authority, and as a result, he is having Nadal on the run and grinding Nadal down, which is a completely turnaround in the on-court dynamic.
So, Djokovic is a tough matchup for Nadal and always has been, but the difference since 2011 is Djokovic's stamina, enabling much better court positioning, tougher mental strength and enabling Djokovic to dictate to Nadal instead of vice-versa.
This is a contradiction of terms. So you're saying that Djokovic always had a technical advantage against Nadal but Nadal had more fitness and physicality.
Guess what? Fitness and strength
were Nadal's strengths over Djokovic [at the time]. In any match between two similarly strong competitors, one player will have certain advantages over the other. Djokovic may have had better technical strokes, but Nadal had better fitness and strength.
The problem here is that Djokovic has improved his stamina, to the point where he now has better technical strokes than Nadal
and better stamina. That means, right now, Djokovic is the more complete and better player.
A matchup advantage is when a player can take advantage of another player even without necessarily being better than that player overall. Earlier in Nadal's career, he would always trouble Federer even when Federer was the better overall player. Why? Because he had a very clear matchup advantage. Taller players like Soderling and Del Potro can give Nadal trouble, even without necessarily being as good as Nadal, because they have a matchup advantage.
When a better/more complete player beats a lesser/less complete player, it's not exploiting a matchup advantage, it's simply being better. Djokovic isn't doing anything to Nadal that he isn't doing to Murray, Federer, et al. His gameplan doesn't really change. He doesn't have some kind of panacea like Nadal does when he hits to Federer's backhand. The only difference is that he's beaten Nadal so conclusively so many times that Nadal is lacking confidence over whether or not he's even capable of beating Djokovic.
That's a mental advantage, not a matchup advantage. Your confusion is that you somehow exclude fitness and physicality from your analysis of 'matchup' advantages and disadvantages when, in fact, you should be including them. Fitness and physicality are crucial skills to have in today's game. At one point, Nadal had much more fitness and physicality than Djokovic, making him the better player. That's not true any more.