While I think it's particularly to care about cutscenes, as they are mostly just annoying garbage you skip to get to the real gameplay at least after seeing them once, they're pretty tough to argue as fair use, because they're generally pre-generated or at least scripted. The content is entirely the creation of the copyright holder. Phil grunting unintelligibly over it or making a Holocaust joke or whatever is at best minimally transformative and unlikely to be considered fair use.
Also, spoiler content, which is what Atlus seems primarily concerned with, impacts the fourth and most important factor in a fair use analysis, the impact on the commercial value of the work. While obviously you couldn't use copyright to stop someone from saying "Rosebud was a sled!" or "Snape kills Dumbledore!" actually posting the text of the pages where it happened in the early days of the release would have less justification as fair use.
Gameplay is similarly a derivative work, but has a lot more claim to being transformative. It is more a work created using the software, including samples of intellectual property like characters, graphics, textures, backgrounds, etc. Even that's on dodgy legal ground, but I think Atlus is pretty solidly in the right about things like cutscenes.
At the very least, it isn't a bogus DMCA strike. They can say completely in good faith that they believe it is not fair use, and could file a colorable copyright claim in a federal court without it being frivolous, even if they ultimately didn't win.