In the attached save file, move the settler north and found a city. Suddenly, the minor faction "Jotus" are ready to be assimilated...despite not having been pacified yet (you can even see that I have a quest in progress for them).

Possibly related, or possibly a separate bug: a couple turns later, when I pacified the village in my starting region, I completed the third ardent mages faction quest. The objective of that quest was to pacify 5 villages; the village that apparently triggered the quest completion was my fourth.

Aha! Apparently there was also a destroyed village in the region that I hadn't discovered yet. I guess it was counting that.