So, as ZLO pointed out in the Q&A, Mass Fabricators still give their adjacency bonus to the Factory if they are paused. It also happens with Mass Extractors. It happens because the bonus is applied as a Buff on, in this case, the start of unit construction, and because Buff type changes are fire-and-forget rather than tracked, turning the units on and off changes nothing. The buff is applied to the Factory on project start.
Strangely, it does adjust when the Fabricator is reclaimed or dies... <-This is the clue: Why does this happen?
So far I am unable to fix this