Karma, how many times does it have to be said, that it doesn't matter what format the textures are in, when loaded there all the same once you're playing a game!
and yes, alpha chanel on the shine map.
the way it's curently implemented, we have the advantage of the tint of the shine map affecting the color of the reflections, but a third texture I think is too much, I was thinking it might be a good idea to use the alpha chanel as a multiplyer of the shine map, you could make everything but the cockpit very dark grey to have a very low effect, it would retain the color tinting properties it currently has, but you wouldn't be able to make un-shiney parts of the ship reflective.
and seeing as we have a fairly good number of shine maps now, I'm thinking it might be a good idea to turn off the the auto-loading of the defuse texture as the shine map, if the same texture is not used in these sections I might be able to make some optomiseations.