Both overlays from Alex's Mobs and Alex's Caves do not seem to affect 3d skin layers.

Notice how the green radiation overlay present in Alex's Caves only is visible at the edges of my character, where a second layer is not present

I dont know what you mean by that.

I don't know which way they used to achieve this effect, but I don't think it's worth it to sink in a bunch of time and code to apply that. Probably neither from me nor from the Alexs mobs dev.