Yeah, I edited my comment a few times but I was going to bring up Bioshock because it has a feature of both integrating gameplay with narrative and a disconnect with gameplay and narrative.
The Vita-Chambers are, as you say, a "real thing" that exists in the lore and is explained in the narrative of the setting, your deaths during the course of the game are "real things" that occur in the story, it's explained away as you using the Vita-Chambers, which ties into the storyline itself. The entire concept of "a slave obeys!" is also based around the gameplay, you can't go around and explore all of Rapture because, aside from the fact that some parts of them are inaccessible due to damage or flooding, you are a slave that can't choose to go where you want.
On the other hand Bioshock sort of defeats its own message, or at least one of its messages, of selflessness vs selfishness. Rapture got to its current state due to selfish objectivism. Saving the Little Sisters is supposed to be a rejection of this philosophy by living for others instead of living for yourself. The problem is that, when taken in the context of the game both options of saving or harvesting Little Sisters can be seen as selfish acts, one of them just also happens to save a little girl, they both end up giving you rewards in the long run.
Searching around a bit it looks like saving the Little Sisters gives you the exact same ADAM amount at the end (which is where this above graph disagrees, but I dunno if he counted the 200 ADAM gift you get every 3 Little Sisters), and you get access to a tonic you wouldn't have otherwise. So you could make the argument that you'd be acting in your own best interest to save the Little Sisters rather than harvesting them.... which sort of defeats the morality of that entire segment of the game. It's supposed to be a choice between selfishness and selflessness, yet the reward for the selfless action is the best one, people could go and save the Little Sisters because they want to be stronger at the end.
A better narrative would be if perhaps saving the Little Sisters did nothing, it was a straight up ADAM lose and made the game harder... the only reward was your own satisfaction for doing the right thing. This is the only time I have a problem with the divide between gameplay and narrative, when the game itself contradicts what it is attempting to say, not the fact that there is a divide in the first place.
Mass Effect has three layers of disconnect. But do I really care that a Krogan can take several shots from my assault rifle on INSANE mode, be killed by a single pistol shot in cutscenes, or require anti-tank weaponry to defeat in the Codex? No, not really. Halo's depiction of SPARTANS also has this between gameplay, books and cutscenes. But that's fine if the gameplay itself is fine. In fact I wonder what this author would say about, say, Soul Caliber, Street Fighter, TEKKEN, Dead or Alive or similar. Do people bitch when they have to fight that liquid Kasumi at the end of Dead or Alive 3, which is supposed to be a hectic showdown, life or dead... and then the fight starts and the two fighters do a best 2 out of 3 and fight on a timer and have an announcer start each round. Do people bitch that the narrative is destroyed when Ryu's final showdown with M. Bison occurs with an omnipotent announcer that demands they fight at least 2 rounds?
I think the problem is that people complain about this disconnect in games that "seem" like they would be movies. The new Lara Croft game would make a cool movie... and so people complain about the disconnect in narrative and gameplay because they start treating it as a movie that you control rather than a video game that occasionally has story cutscenes. Tactical shooters have almost no disconnect between narrative and gameplay, so some video games already provide the scenario the writer above wants... but not everyone wants that scenario and not every game needs that scenario.