this might be impossible but it would be cool if we could use 32 bit textures both with their alpha channels and without them. that way you could have it look like one texture with transparent parts and one that's solid but you'd only have to have one texture in the database and people would only have to download one and clog their video cards with it. i would use this feature alot and if you add in tinting it would make it easier to use fewer textures over all.
i'm picturing a menu like shiny or a checkbox in the texture window for any 32 bit textures with alpha channels.