xLODGen is a tool mode of xEdit. While archive loading is an option in edit mode, the lodgen mode should have it enabled by default. If you have any issues with loading plugins, or archives, test with xEdit and in case there are issues report them via xEdit github issue or on the xEdit discord.
If there is a problem that only happens in LODGen tool mode, upload the log here and provide concrete information or the plugin and the BA2.
xEdit/xLODGen loads BA2 via sResourceIndexFileList, sResourceIndexFileList, sResourceArchiveList, sResourceArchiveList in Fallout4.ini, Fallout4Custom.ini and of course via the usual [plugin name*].BA2, which is the normal and preferred method to load archive files for mods/plugins in the game and all tools.
plugins.txt is created by the game/mod manager to know which ESM, ESL, ESP to load. Whatever plugins are enabled in it, will be used to look for matching [plugin name*].BA2.