I'm not sure about 3d texture handling, but in the 2d realm you should be able to choose between masked blending (choosing a mask color) and alpha blending, so if you go for alpha instead you may end up having more control over it? However, I'm not sure if I understood your question correctly... no matter what, you'd have to consider the alpha in your painting process and either paint color|alpha or choose an off mask color to paint on it. (Oh dear god I could be so wrong!)