I'm sure you could use the texture pain tool, but o think you're best off using vertex color as a mask instead of a spalt map. this would require a cgfx or hlsl shader in Maya but is a much better solution.
well with vertex colour you can share the same material and textures across lots of meshes, and instances. in unity it is possible to get a plug in that let's you paint vertex colours in unity so you can also paint instances of meshes differently too. the way to get around it only applying to verts, and causing gradients…