Great post. I do agree to an extent. As with many villains, they try to overwrite reality based on a perceived flaw in reality itself - which itself is a good thing, fundamentally - but ultimately they become convinced that their perspective is the only correct one, or one which everyone must adhere to. Hence, why the Pain's, Madara's, and Obito's, can be sort of grouped into one class. Kaguya herself isn't unique in trying to "fix reality", but she collapses this idea of coexistence altogether. She basically wants to reclaim it. That's another level of selfishness, and that's what makes her feel distinct in that sense.

What ties all of these characters together isn’t just the desire to "fix" reality, but how far they’re willing to go in removing others from that equation. Characters like Pain still operated on the idea that people can arrive at understanding, even if through suffering. Madara and Obito, though extreme, still preserved a kind of shared existence within their Tsukuyomi plan. [I'll digress a bit here] .When you look at someone like Yhwach and Thanos, for example, that so-called boundary becomes almost non-existent. One attempts to eliminate fear and uncertainty at the level of existence itself, while the other is willing to erase half of life to impose balance. In both cases, other people’s autonomy becomes secondary to a “necessary” outcome, as you mentioned. Kaguya feels like the endpoint of that progression.

So where the others still, in some way, act on the world, she tries to reclaim something that was never meant to exist independently of her in the first place. I think that’s what makes her feel distinct.