You wrote a post on the GLScene forum, so maybe yarunderoaker will help you.
For me it is too complicated and I think it is better not to use GLScene for this - just write a tool to create any texture you want and then insert it to GLMaterialLibrary.

Another solution is to write your own shader material and use transparency of mask file (.png) for the final color:
gl_FragColor = TextureColor;
gl_FragColor.a = MaskTextureColor.a;