BSAs can't override each other in Fallout 3, this feature was added only in Skyrim. Previous games require custom xSE extensions to implement that. For New Vegas this is done by JIP LN NVSE extension (read about .override files) https://geckwiki.com/index.php/BSA_Files#Notes_2 No idea if something similar exists for Fallout 3.
Can't be fixed unless someone will manually readjust positions of troublesome cliff refs in the entire worldspace (there is a mod for that for Skyrim). And even then it will lessen z-fighting, not remove it completely.
Objects LOD consists of merged macromeshes covering 4x4, 8x8 and 16x16 cells depending on distance, there are no separate objects and hence nothing to select. No idea what screenshots you've seen, but it was not selected LOD for sure.
Use hex editor to replace a single letter like "BstomaCompanion.esp" for example in the plugin's header, create an empty plugin with the same name to server as a fake master.
"Is it really THAT hard to just duplicate a worldspace with EVERYTHING in it?" Yes, everything involving a new worldspace creation (either from scratch or duplication) is one of the hardest tasks. You can't just copy worldspace in xEdit and expect it to work as is. This requires a lot of additional clean up postprocessing by someone who knows very well how the engine works.