Enabling this will give MusicBee permission to move and rename all of your files.
The fact you've referenced that other ten year-old thread suggests it may have already done that.
If so, I hope you either have a backup of your files, or were satisfied with the results. From memory it is also complicated by having files in two different drives or directory structures, as your screenshot indicates you do.
OUCH.... as Zak suggests you didn't do yourself any favors by starting out with those settings after admitting "I'm new to MusicBee and need some help organizing my large music library. I've got thousands of tracks spanning various genres, and right now,
it's a bit of a mess.....
I’m not sure where to start."
If that is the case, you're far beyond any "plugins," etc. As Zak hinted, unless you are actually OK with what has already happened, your best bet may be to call it a learning experience and completely uninstall MusicBee and replace the state of your music files with the backup you surely must have made of them before you began. Then, re-install MusicBee (preferably with the easily updatable and backup-able Portable version), and be sure none of the automatic file handling--"auto-organize music library files" and "automatically sweep and organize new files"--is enabled. Neither of those is checked by default, BTW, and the first one even produces a warning message when attempted. Then, once you get a "feel" for the whole MusicBee library concept and what it allows you to do/display/organize on a purely virtual basis within the application, if you want to go further and try the physical moving/renaming options you can ease into it and be much better off than you probably are now.