You should be able to put the lightmaps that you generate yourself from Blender into the same material lightmap slots. There's no support currently for generating UV2's or baking lightmaps directly inside of Torque3D. We had planned once on integrating pureLIGHT directly into the Torque3D editor but those talks fell apart years ago.
I don't remember all the details of how the Torque3D lightmapping works, its been many years since I last looked at it. There were flags to indicate which lights were included in the lightmaps to avoid double-lighting meshes. I don't know if much has changed since then.
I did experiment once with changing the way Torque3D internally stores its lightmaps. It wasn't too hard to make them assignable per mesh and point them at a part of a larger lightmap atlas instead of a separate texture like it currently requires. I believe I still have the code for doing that kicking around on my computer, though that would have been for a version of Torque3D many years old by now.
If you've still got the code, I wouldn't at all mind having a gander at it. I've been mulling on getting baked lighting back into the fold for 4.0-ish, so anything that'd jumpstart on that would be incredibly useful.