Pc0de, 2 quick questions:
1. When you assign the new material to the "joined-multimaterial" mesh, do you first create a temporary mesh, like a cube, to assign it the auxiliary empty material to it, and then select the mesh with the multi-UV mapped materials and assign it? Or do you simply select the multimaterial mesh and select the "add new" option from the material dropdown list? (in which case, it clones the actual material in the list).
2. If you're assigning a white material, created on a temporary mesh, to the multi-material mesh, do you get the active material replaced by white as on my next screenshot?
With this material replacement, I seem to be getting better results, the 2 layers seem not be merging into a single one but I still get a patchy grass, and the material replaced by white seems to be left out of the lightmap calculation

(yet it's reading the diffuse map UV info).
Man! I gotta find a way to achieve your results! they look great!
On to more testing.
regards,
Alvaro