I believe this is an unrelated issue to the alpha map problem outlined in this thread.
I have come across this issue in earlier versions of Enscape.
My theory on how Enscape handles decals from Revit is that Enscape makes the decal inherit the material properties of the surface it is place upon. So it won't change the opacity of the surface but instead only change the color of the surface.
What would would be great is if you can have a decal be opaque but also clipped with the alpha texture when placed on a transparent surface.