I never thought of diagnosing mod conflicts as placing blame somewhere, just trying to solve a problem. Like I said before, deleting textures from the MMM folder was affecting the textures on the FNV super mutants, so the two are clearly connected. Also, the texture pack I use shouldn't have anything to do with this since NMC does not affect enemies or NPCs, only landscape and objects. Uninstalling NMC had no effect, either.
I took my archived installation as it was before I installed MMM or any texture packs, where the super mutant textures were fine, and installed MMM on it. The textures are now overlapping there just as they are in my main install. So it's obviously MMM. It must not be getting along with something I have.
With MMM installed, when I rename my textures folder and Verify Cache, I get FNV super mutants with half missing textures as in my above screenshots. Putting the other textures and folders in didn't change anything other than restoring the half-FO3 textures on the mutants when I put MMMFO3's textures back in.
I'm going to take my pre-MMM install again and install MMM folder by folder or even file by file if that's what I have to do, so I can find out exactly what file or files are doing this.