I don't quite understand your problem. I do not need to paint the background the color of the glow at all, no offense but I'm quite sure you're doing something wrong.
The layer beneath should never be a layer that blends with the transparent background with some kind of effect, as that won't have any effect inside 3DGS. TGAs save transparency and also color, but not if it should multiply with everything beneath it and so on.
Can you describe step by step what you're doing? Perhaps I can solve your problem.

because transparent will turn white.
As far as I know this happens with 24bit TGAs only.
Cheers