I downloaded your game and looked at it, played it for a turn and triggered the Domination, just like you said. I'm befuddled. I ran the .sav through Mapstat. Territory is 82/451 and population is 24/99, the first numbers what you have and the second what you would need (both) to trigger Domination.
I've never played this mod/scenario before, but I'm going to go out on a limb and guess that maybe the Domination limits were somehow adjusted by the designer. It might could be your score, too, it's significantly higher than everyone else. Again, I am stabbing a major guess here and would have no idea how to confirm it, I'm not that familiar with the editor yet...
EDIT: I've never played something with Victory points before. Is it possible you held enough long enough that you hit some sort of victory point win condition that was just coded to appear as a Domination win?