I feel like it also has to do with lots of games featuring elements of (or full-blown) violence as part of their regular gameplay loop.
Yeah, in Helldivers 2, you're committing genocide for insidious political reasons. But in Pokémon, you're committing genocide, because you're a ten year old and your neighbor gifted you a pet.
Normally, the genocide part would be the very obvious red flag for something political going on. Instead, you need to be aware of why precisely you're doing the genocide this time around.
Such genocide elements are usually also paired with fun gameplay (because violence is easy to translate into gameplay), and with a terrible story, so it's understandable that people would skip all the story elements.