I think the overarching point is that "storytelling" simply can't work in the same manner as it does in books and movies.
If you tell a story in a cutscene, you then aren't playing a game at that point. Or if you plot out every possible interaction (kind of like The Walking Dead games) you have to limit the outcomes to a manageable level, which hamstrings the gameplay. So what's the solution? The article is arguing that you have to abandon narrative and focus on what you want the player to feel directly.
The problem is that "game literacy" is focused on all the wrong elements. A game like Doom has much better, tighter, more interesting gameplay than something like The Last of Us. (which I still really enjoyed!) And you can be moved by the story, characters etc. from The Last of Us, but it's a lot more like how you feel watching a movie. With Doom, people create their own narratives by interacting with the game, and those narratives have a different kind of power. People still tell stories about playing Doom for the first time 20 years ago with their friends. The objective, I think, is to make a game where those personal stories are directed to achieve a specific effect.
There's one example of this effect that I've read about before. There was a game in the 80s where you play a war game as either the U.S. or Russia. If you play as the U.S., you stockpile arms and try to win the war as you'd expect. But if you play as Russia, you have a whole different set of concerns - starvation, winters, limited resources, aggressive neighboring countries and other factors which lets you experience some of the desperation Russians must have felt during the Cold War. It's a pretty powerful story to tell through gameplay alone, and a story that was told through gameplay without narrative.