So after working on this all day, I found a solution. Probably not the most convenient solution, but it works today on Win10. This is ideal if you want to create lightmapped environments with an early 2000s level of polygon and texture detail. I don't think it will work for much greater detail than that, primarily due to import and lightmap limitations of Map Scape 2.
You need 3 programs: Blender, Ultimate Unwrap 3D, and Map Scape 2
1. Build all your meshes you want to use in your map in Blender, with stage 1 UVs set for base textures. Export each as DAE
2. Use Ultimate Unwrap 3D to convert each DAE to X
3. Build your scene in Map Scape 2 by importing the X meshes and using the primitives in the program. Generate a lightmap in the program. Export to DBO.
4. Use Ultimate Unwrap 3D to convert DBO to DAE. Make sure to double click each material, click map tab, set diffuse texture to composite and in the properties, set the UVMap for the lighmap to UVMap 2. When exporting, check the box to export the groups as meshes.
5. Load the DAE into AGK. Texture by mesh, applying each base texture to stage 0 and the light map texture to stage 1. Make sure to have texture filtering enabled to get a smooth looking lightmap.