That doesn't make sense :(
When building LOD, xLODGen goes through all the references of STAT, SCOL and ACTI records in worldspace, gets the winning override, skips refs that are
1) Deleted or disabled
2) Enabled via parent (have XESP subrecords) except for those that have "Megaton" in EditorID of parent
Gets the model file name from the base object, adds _lod.nif at the end and checks if that file exists in the current loaded BSA archives or Data folder. If yes, then this object goes into generated LOD using position/rotation/scale of the reference.
So the only way some object will be missing in generated LOD is if winning reference override is defunct according to above rules of there is no _lod.nif mesh file.
Anyway, I can't verify what MO does. Since I don't use it myself, it is up to users to make it work. I know for sure only one thing about it - management of BSA files in MO must be switched off, it prevents xLODGen from opening BSA archives which hold _lod meshes.