Ever find a fix for this by chance?

I've been doing some custom species projects myself and discovered the same issue. My custom model (based on the original Anthro Survivors Cat) have missing faces on the model after wearing any additional, second layer clothing. Same problem occur in vanilla models, I noticed. I checked everything in blender but all weightpaints, layers etc. seems to be okay. For now, this issue is unsolved.

I think the issue is the weird interactions that are possible under certain clothing settings combinations. They may be configured such that their combination replaces the texture rather than goes on top of each other, so you get transparency without any body texture underneath.

I managed to fix it. The problem was in the UV mask/map layout.
Clothing that are mesh that game puts on your character (like sweaters, jackets etc.) have a predefined mask that hides some part od playermodel textures. Those masks are very strict when it comes to what faces to hide or with not. It takes only one pixel of the incorrect part of the mask being in a face of f.ex. head UV to make some parts of it invisible.

Look at this example (this one I fixed myself):
https://pasteboard.co/LlFo1KY2hVDE.png
I just adjust the position of few points and basically fixed the issue completly. Then you just need to slightly change the texture file (if your changes really caused any distortion) and that's it.
Problem solved.

引用自 Benszasty：

I managed to fix it. The problem was in the UV mask/map layout.
Clothing that are mesh that game puts on your character (like sweaters, jackets etc.) have a predefined mask that hides some part od playermodel textures. Those masks are very strict when it comes to what faces to hide or with not. It takes only one pixel of the incorrect part of the mask being in a face of f.ex. head UV to make some parts of it invisible.

Look at this example (this one I fixed myself):
https://pasteboard.co/LlFo1KY2hVDE.png
I just adjust the position of few points and basically fixed the issue completely. Then you just need to slightly change the texture file (if your changes really caused any distortion) and that's it.
Problem solved.

That's *A* problem solved, but not the one the OP was talking about.
The actual issue with things like fishnets is that the textures for them have some semi-transparent pixels around them that, when applied to a normal body, form an anti-aliasing effect. Anthro bodies, however, are a separate mesh, and when those clothing items get put on, the texture is applied to the invisible human body that's still there, and the transparency of those outer pixels OVERRIDES the texture in the furry model, instead of combining with it.

here's an example of that they're talking about:
https://pasteboard.co/0lPkjZjNuhn3.jpg