Ok, so is there really only one executable with command line parameters for the different modes? Can you post the setup somewhere for those that just wish to run the executable with the different params for the different modes?
Yes there is and you already have it.
You can literally just rename TES4LODGen.exe to TES4Edit.exe and run it and it will be TES4Edit. Or rename it to FO3Edit.exe and run it and it will be FO3Edit. It looks at it's own file name and behaves accordingly.
Is it safe to assume that whatever the final enable/disable state of an item is according to the Rule of One is going to be considered before the program generates the VWD data?
There should be no difference in behaviour in this regard from TES4LODGen 2.x
Obviously, any object that is being enabled/disabled during the game is a huge problem because .lod files are static and do not retain any link to the FormID of the REFR that defined the object.