Why do some mod textures disappear if I disable vanilla textures?

[InDarkestNight]

I've found a trick to finding which textures still need replacing. I've been doing this by just 'hiding' the 'textures.bsa' file. I was inspired to do this after seeing an SE mod that was meant to help in the same task by replacing all vanilla textures with brightly colored squares.

However, I've since found that this also disables textures from mods. The first thing I noticed was that all trees appear lavender. This is odd, since I'm running Enhanced Vanilla Trees, which I could've sworn used new textures. I figured that maybe it just replaced the mesh which was doing something weird to the vanilla textures. However, upon screwing around I found more were missing. In particular, I found that various weapon sets were appearing lavender, leading me to think that Book of Silence didn't support many weapon sets. However, upon looking at the mod's files, I found that it does in fact retexture the various weapon sets that had missing textures if I disabled textures.bsa. These included falmer weapons, dwarven weapons, and maybe elven weapons. I also found some of its creature retextures weren't applying. Its armor retextures though were working fine (minus missing some maps, like the one that determines shininess). I also downloaded a mist replacer because I got sick of not being able to see anything in draugr tombs due to giant purple squares being everywhere. However, without vanilla textures enabled, it doesn't do a damned thing! Also, I did find that installing textures for things I thought were missing, MO2 often told me that it was overwriting another texture mod I had (sometimes even overwriting everything the other mod had)!

Why would this be happening? I thought I had a way to find textures I had yet to replace, but its increasingly looking like my idea isn't actually working. What else am I supposed to do? Of course, right now I have just about everything replaced that you can find a texture for. Now I'm mostly just missing various pieces of meat and minor clutter. It got the point that even without vanilla textures, my game often looked perfectly normal with just mod textures. Seriously.

Edited January 22 by InDarkestNight
typos

[xkkmEl]

It could be that the mods are only replacing the base texture, and leaving the normal maps and other adjunct textures intact.  There are like 10 or 11 textures you can layer on any given pixel.  Another possibility is that the mods are overriding the textures referenced in the nifs with texture maps in the esp/esm.

Without looking at a specific example, with a well identified nif, and applicable texture maps, it'll be hard to give definitive answers.