There used to be a mod that didn't replace any existing town, but added Naga. Maybe you could improve it?
Posts from = Mods that replace individual factions =
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they could have been placed on the map, but they weren't in the game
Could you move everything that's in the Naga faction to replace the ones that aren't being replaced?
or better yet, make them a separate faction!
It will take a long time, but it's worth a try.
a mod called Crimson Necropolis.
By the way, I noticed that the mod affects not only the Necropolis.