Howdy,
I apologize for being late to reply here. From what I have read so far, it is possible that there are save game files hidden away in the computers that will have mod data that will continue to "contaminate" your game even if you delete the mods. That being said, to my way of thinking it seems that one would have to perform a complete search and delete of every BG 3 file on the computer. Then to be safe, restart the computer and reinstall the game. I could be totally wrong about this; however; that is what I will do if I decide that I wanted to get rid of mods for the sake of achievements. I am 78 ( 79 in July) and honestly, I need some of the mods as my hands are not all that flexible and my mind is slowing down.
The above script extender may work, but I think that I read that it is for Windows only, I have been using Apple boxes since 1980.