It would seem like that. But If I remember correctly what I read somewhere about them, I believe the unofficial patch team's intent is to only fix bugs and make corrections in pure vanilla game as it was designed to be and it was never Bethesda's original intention to allow three factions to survive in peace. So If anything, if that's true, it's actually surprising that they didn't try to include a fix to undo that possibility. But they probably realized they would have a riot on their hands if they did so.
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Sorry for the Necro :)