Ok, I think I figured out a workaround to the transparent image problem.
I created another face 1/1000" in front of the surface of my ship that I wanted to apply it to. I projected the decal and painted the material onto THAT face, so that when you see through the transparent bits you're seeing the 'real' face 1/1000" behind it. As long as your surface isn't extremely curved, this should work without hours of building out a new surface. I also hid the edges of both surfaces. You'll also have to decide on the color or material of the surface, because changing it would in my mind require that either you go into the model and change the colors from the inside, or you would need to delete the face with the decal on it, change the color, then rebuild and reapply the face.
I've tested this in the Twilight Render plugin as well as Kerkythea, and so far so good...
Now I'm off to make weathered insignia and markings for my fighters! I'm going for the battle worn X-Wing look, and on old plastic models I'd simply use fine grain sandpaper to sand through and rough up the decals a bit. This is slightly more involved, but I think I finally found something that will work for me!