Investigating one of the missing pieces of Overpass "HWDoubleEndCapR02" (0x7485b) in Cell 0xdbe0, I load my entire load order in xEdit and navigate to this record:
It appears there are no overrides to this piece from any mod in the LO. There are 3 LOD levels with 2 different meshes defined.
Next, I load all the BA2 archives in my Data folder into BSA Browser and query each and every BA2 for "HWDoubleEndCapR02_LOD". Expectedly, I get a hit in Fallout4 - Meshes.BA2:
I toggle through the rest of the loaded BA2, and there are no more hits for that piece. Apparently, nothing from any mod BA2 is overriding these vanilla LOD meshes.
Next, lets see if there are any loose files in Meshes\LOD\Landscape\Roads...
Nope; The respective folder does not even exist in the file system. At this point, it is pretty safe to assume that there are no overrides to the vanilla LOD meshes for this piece, at all.
So let's investigate one of these LOD meshes in Nifskope, to see what materials or textures it uses:
Querying for HWOverpassLOD.BGSM on all the BA2 archives in the Data Folder:
One hit is returned for Fallout4 - Materials.BA2.
Another hit is returned for FO4LODGen - Main. No other hits can be found in any BA2, pertaining to this file.
Checking for any file system overrides:
Nope. It is pretty safe to assume at this point that the material file from FO4LODGen - Main is being used, since the FO4LODGen.esp is lower in the LO than the Fallout4.esm.
Let's take a look at this BGSM:
Checking for the respective textures:
and
The filesystem doesn't have any loose files overriding this either, as I don't have a LOD folder under textures:
So let's inspect the textures in that NeuraLOD BA2:
Yep, they're there and can be loaded, by paint.net at least.
Now, after doing all these checks, I don't see why my generated LOD is generally very incomplete and specifically missing this particular piece of Overpass.