I think a prime example is in the lesson recently released on the E blues shuffle. You can see during the A5 chord, that the E (6th string) is not muted by the left hand and therefore it "must" be muted with the right. The first time through, I didn't notice and found myself using the thumb to mute it, not my right hand.
I think both are ok, but I wanted to do it as demonstrated. Right hand muting has a lot to do with the how your guitar fits and the type of bridge and everything so it is hard to show exactly what is going to work for any individual. But I know I would have liked to see how he did it, even though I eventually worked out a way for myself.
So when I went back through the lesson and used the triplet count and purposely made a small sound to mute on the middle note in the triplet count, it was a big challenge to play in time and "mute in time" and keep everything even.
It is a subversively complex lesson composed from simple elements!