ok, now I see what you're saying.
Well how about this then:
You have seperate skin files for each element of effects for the engine.
Like you'd have mySkin.png and that'd just be the basic skin.
Then you'd have sperate files which are basically just an alpha layer with the extention changed:
mySkin.bump.png
mySkin.relection.png
mySkin.magicalsparkles.png
I know, I know, I know -- it's extreamly bulky and takes up a lot more space, but it'd be good for organization.
Another idea would to be the inclusion of a skin tool in the game where you can just paste in each of the layer effects for the texture, and then save it as a special T:V filetype. Personally I'd like that idea the best, but we all know that in the past game companies aren't too quick t release useful tools to the community.