The issue is with how you used the alpha of the texture. You don’t plug that into the alpha input of the principled shader unless you want parts of the mesh to vanish. When you are mixing textures you plug that alpha into the factor of the mixRGB node like this:
textures.blend (686.6 KB)
The only reason no part of the mesh became transparent when you plugged that into the alpha socket was because you didn’t have transparency enabled in eevee.
I wrote a brief guide on how to emulate photoshop layers with nodes some time ago. You might want to take a look at it: