The premise of the commentary is that players tend to lack empathy for fictional entities in games just like the Typhon lack mirror neurons, and so the purpose of the Talos 1 simulation is to engineer situations that prompt and test the player's empathy for doomed characters who may even deserve their condemned fate. This video makes the argument better than I can:
The problem of the game is that a joke needs first a preparation part that culminates into a punch line, the same as a joke, the ending of Prey is the punch line where there never was a preparation phase in the first place so it feels random and makes no sense. If the game was a simulation intended to provoke emphaty, it failed hard at provoking anything then the game judge the results of the simulation as if the player failed the emphaty test when it was the game that failed the emphaty test, not the player. Emphaty isn't an automatic thing among humans even on real life and not only on a virtual context about virtual entities, we first need to recognize the humanity on the other person first before we can feel emphaty about that person. (there are many ways we can fail to recognize the humanity on the other person that allow us to do terrible things). I don't think the game designers understand how emphaty works.
The game characters are very removed from the player, distance, especially removing physical presence is a sure way to guarantee lack of emphaty, just look to the Milgram study, you can hide an unknown person behind a wall and have someone in authority telling to this person to apply lethal shocks to the other person and 65% of people would do it. So, when I didn't help doctor Igwe, I didn't care because: "Who is this guy anyway?" then the game judges me and said I failed an emphaty test and humanity is doomed, the Thypoon will ever learn emphaty. You know, I was furious at the end and was thinking "Dude, how about you actually test me first before claiming I failed a test you didn't bother to make?
If they wanted the end to work, they should have redesigned the whole game. The end isn't fitting the game they made.
I can agree that it can feel a bit deflating for a game focused on immersing the player in a fictional environment to call attention to the fact that you're just engaging with simulacrum, but I think Prey deserves some credit for what it tries to make of the idea. I'd much sooner criticize the the dull audio logs and lackluster story beats prior to the ending, because I struggled to engage with Prey's fiction over any of my three playthroughs, while games like Deus Ex still capture my attention with details that I overlooked even after I've thoroughly dissected that game.
Deflating is an understatement, they said all you did was a simulacrum AND you are no different than one of those mimics that was just fooled into thinking was human, pretty much burning to the ground all relevancy of the plot, they not only did a 360º turn and return the story to square 1 but they actually gone negative when they claimed you didn't even exist and were a random Typhon experiment subject without even a name. The protagonist of the story didn't even exist. All that, for their meta commentary about emphaty that couldn't work anyway because the storytelling of the rest of the game failed hard into supporting that.
If you failed the emphaty test ( that they failed to apply in the first place), the plot is even more irrelevant.
Prey keeps track of nearly every relevant permutation of interactions with NPCs in the story. If you pre-emptively kill January, December will be your guide through the game instead (though not as fully implemented as I'd have liked). You can fail to rescue Mikhaila and/or Igwe and dialogue will change. Go to the Cargo Bay early through the G.U.T.S. and Elazar will contact you to say the area is on lockdown. Most of it builds up to the presence or absence of some dialogue or event (e.g. you have to have rescue Igwe and incapacitate Dahl in order to escape on the shuttle, rescued characters will be on the shuttle, etc.), but the game still manages to make every accessible NPC mortal without breaking the story. Admittedly, they cheat by locking Alex in a panic room, but it's a nice effort towards handing the player the reigns.
I agree that for the standards of a AAA game, this sounds great but I already seen this kind of dialog reactivity since Deus Ex so I'm not exactly in shock about how they implemented reactivity on this game.