Hi,
I might be off base to the problem you are having, but you can get rid of the alpha issue if you create a base layer and then add your paint layers on top. For example, create a fill layer that sets the specular to black or a base value. At this point, you have filled the texture with a base value. Then you can paint onto of this base and when you export, you won't have to worry about alpha.
Cheers,
Wes