There shouldn't be a physical second uv mesh layer in the geometry of the .x model. As I understand it with my limited knowledge it is a 'phantom' uv layer created which overlays the original and can have a totally different uv layout. This can be seen in the lightmap itself which is obviously an auto unwrap and totally different from the models original uv layout.
If you look in the lightmaps in the testmap folder you can see this and the .dbo files which accompany these. i can only assume these are the terrain lightmaps and the supply crate with wooden crate (long)
This is the unwrap for the supply crate.
Now, if you open these .dbo files in a modeling app you wont see any mesh but they do have a face count, if you add a tessellate or turbosmooth modifier they will increase the face count so though they don't have a physical presence and appear as phantom they do add to poly count. You would only need one unwrap per model so if you had a dozen of the same only one model with several different lightmaps to do the job, all the same you shouldn't be seenig multiple objects for the terrain 'blocks', at least I assume that is what some of these objects are in the folder though they might be LOD meshes from the models which shoudn't be created since you only require the highest LOD to lightmap. I can only guess with this one
This is something I discovered when I was reading about a bug in the autodesk .fbx converter back in 2013. In some blog they were discussing this bug and how they could convert to .dae then select faces to apply textures and effects on different 'layers'. they believed it was a single mesh. A plane with two faces, they were applying a material with three layers to the mesh and on converting to dae from fbx were believing this model had only two poly's but you could select three material layers.
Of course I had to dig into it and found that it actually had six faces in the model but when selecting sub object it appeared to be one single mesh. When I applied a turbosmooth modifier to it all the faces split apart and I could select the sub object faces. There were in fact three planes in the model.
I used this in the skyspheres I have been creating where I discovered you could create these meshes physically and have them occupy the same space for effects which overlay each other.
The reason I go into all the above is because I believe in the same way as you can create non physical vertex geometry in a shader to apply textures and effects to (this can be seen in the skyscroll shader where a plane is created) I reckon the same sort process is used in lightmapping.
I have imported one of the dbo in the lightmap folder and it is difficult to tell which is which but the one I did import had over 9000 faces even though it doesn't appear in app.
I have no idea why some models aren't unwrapping properly in the lightmapper but it isn't because of overlapping uv's in the .x. Just about all the stock models have overlapping uv's and most lightmap just fine. It may be something simple like model parts all being separate on export or maybe some other reason, I wouldn't have a clue at this point as they aren't my models and I have no idea what app they were created in
I will all the same try importing the supply crate and take a closer look at it, I have found sometimes that little bugs can be fixed by importing and simply exporting again to fix things. Some exports can be radically different in export data contained in the model file, as seen with fbx having different data over different versions in the export module which some engines get confused by.
It is kind of strange since I have found that with at least one test lightmapping there were no .dbo objects and only the maps in it, most of the tests I have done produce these 'phantom' models but on one occasion it didn't. So maybe this will help give you a clue as to what is going wrong.
edit*
Took a look at the supply crate model, it has three mesh layers but I cant select the single sub object meshes which I assume may be LOD levels, maybe this model was collapsed to single mesh before export in error, when you do a lot of models you sometimes make mistakes. As said I cant select these meshes as single objects so cant fix it, the original author should have files to go back to and try exporting it again.