I very rarely use the maya software renderer so unfortunately can't help you there. I can understand the convenience of painting the alpha interactively. What I would do:
First I'll get the UV's back into the 0-1 space, use the repeat UV attributes on the place2dTexture nodes to tile the texture, paint the alpha and once satisfied, export the alpha values of the vertices to a texture. (In the paint vertex color tool, under the attribute maps section) I would use this texture as a starting point in PS as an alpha channel on the "rust" texture or even use the texture as is for the alpha attribute in the layered texture.

I'm sure there must be other ways of achieving this so I'm throwing this open to the other gurus on this forum.