After ALOT of research, both the NWMax & MDLOps are unable to work with lightmap-enabled module MDLs. The MDL needs to have its standard diffuse texture along with a lightmap texture in order for it to work.
The NWN MDL compiler is able to output proper module MDLs, but it doesn't currently work with Kotor. This explains why M478's modules look so...bright. Contacting cchargin to see if he can add in a feature in order for this to work.