I didn’t know about the gas mask stuff, I have the Air Filtration CBM but I still had debuff so maybe gas mask is mandatory. Also I thought the NPC’s bugged out and were not following me, I did get them eventually to exit the tower without gas masks by moving around the tower a lot.
I’d say fire is pretty good as well, you can throw the Molotov or spray the flamethrower when you enter the floor and the mi-gos will stay back since fire scares them. Then you can shoot them without worries (I remember the big mi-go guards were hard to kill otherwise when in big numbers).