Sorry, I should have worded stuff more clearly. I have done that, and setting bUseMultibounds in GECKcustom.ini to '0' fixes the maps in GECK perfectly*. I tried putting it in the fallout.ini and falloutcustom.ini to see if it has the same effect but no luck. Probably for the best it doesn't work though, because of the Lucky 38 needing it.
*The glitchy parts of the cells in GECK when it wasn't off were 1:1 with the glitchy parts of the cell in game.
Still, I am now even more confused now that you say that only the Lucky 38 uses multibounds. I was thinking about removing all portals/multibounds in FreesideKingsHouse, 2CCampGolfResort, etc., in GECK and see if that works. But if they don't actually use multibounds then that probably wont work.