What Meridian says is true mainly for base living quarters. Unwanted objects are not difficult to remove. Corrections to the text of the mod will be minimal.
But the Men in Black will be a bit tricky. They have a lot of missions, prescribed in different files mod. Need to find them all and remove.
But that's not all. The Men in Black must have some place in the exploration tree FMP. And it's quite possible that without encountering these enemies once, without researching them and their equipment, you may not be able to access any other meaningful research.
When creating a large mod, each part of the mod is assigned a role. And sometimes simply removing something will leave too big a hole in the gameplay.
But I can't say unequivocally. In the Final Mod Pack I played a long time ago and one of the very old versions. I don't remember the details of the research.