I think fbx as a format supports multiple sets - it certainly supports <n> layers of data. I'm not sure that any of the major exporters/importers handle it though. To store the color in UVsets you can use channels in max, I'm not sure if there's a way to do it through the UI in maya the path of least resistance is to pack…
When a cage is used the lowpoly vertex normals are ignored for projection and instead vertex will point towards their twin on the cage model. Since we want them all looking at the same tiny point in space we just shove the entire cage into that same spot. Scaling to 1% instead of 0% avoids bits of the cage getting merged…