I've noticed tribes having multiple settlements, but also there being multiple tribes with the same color. This can get reeaallyy confusing. Could you look into making sure maskling tribes can't have the same color? Or if they do they're all one big group?
Side note (When modding how do you make a race that auto-gens and isn't just created by you playing it? Is that in the javascript file?)
AI Tribes pick randomly from the available colors, sometimes there just aren't enough to go around.
During world generation AI tribes are placed, those are defined in the XML files. "wg_ai_placement.xml" in BaseMod defines the placement of the masklings. The ai_placement element defines what biomes the tribe will prefer, what territory size they'll prefer, and what javascript functions to use for generation and ai. I'm not sure how well multiple races will work, I haven't had a chance to test that yet.
