I wouldn't say GTA counts because the gameplay shifts into more of an open-ended sandbox. The choice of the player to act somewhat incongruous with the narrative is, or should be, an understood and optional liberty. And even then, it's not terribly incongruous when stuff really hits the fan later on. And a lot of the crazier stuff is unlocked behind progression walls anyway. In other words, while it facilitates ludonarrative dissonance, it isn't inherently dissonant.
This is in contrast to gameplay that directly and inherently clashes with the narrative, like in, say, Uncharted or TR13.
It's not the most important part of a game in most cases, obviously, but it's certainly a valid criticism. I agree with the video. Uncharted rubs me the wrong way particularly due to its patronizingly hunky-dory narrative even though it's objectively little worse than something like TR13 -- which comes off more as clueless. It's like Indiana Jones with no finesse and entirely up its own ass. Tibet, in Uncharted 2, was jaw-dropping for all of the wrong reasons. "Bye guys!" Then it ends with Drake killing everyone but the main villain because Drake wishes to prove to himself and to the villain that, in spite of his anger, Drake isn't the cold-blooded killer he's being purported to be. It pains me to know that this writer also wrote much of the Legacy of Kain series. Granted, if it were a stronger game, the narrative issues could be swept under the rug for me. Likewise, if the narrative were stronger or more congruous, it would present a more positive context for the somewhat mediocre shootbang to be enjoyed.