I've had catastrophic disasters with music libraries handled under iTunes, dropped it years ago. Musicbee is hands down the best music library, if not foobar2000. Not an Apple user but iPod is the only device I like to use but I dread installing iTunes just so that I can use Rockbox. I do not use the iPod plugin because it force involves the use of iTunes. What I do is open the latest itunes.exe using 7zip and only extract and install the iTunes64.msi and AppleMobileDeviceSupport.msi for lean bare bones support for iPod USB connections to restore the iPod.
Because Musicbee has a unstable connection under a Rockbox USB music sync, where the connection drops every few minutes while syncing; what I do is
uninstall Rockbox bootloader (not delete .rockbox folder)
reset iPod by holding Menu + Center, and immediately before the Apple logo appears, turn the hold switch on, and the iPod reboots back to normal default "white" interface, sync the iPod under Musicbee as regular flash drive connection to /Music folder, and then
install Rockbox bootloader back
reset iPod again normally without the hold switch to boot back to Rockbox, all while leaving the internal drive /Music untouched. The USB connection sync stability is flawless under the regular iPod interface as "flash drive", but once you have your full library in sync, one could go back to Rockbox and sync the occasional minor sync. Syncing the occasional song or album under Rockbox should be quick, if the connection drops, just hard reset back to Rockbox and connect again (hold Menu + Center). None of the "flash drive" sync music will appear under the iPod default interface, for that you'd have to use and turn on the plugin, make sure all the iTunes settings are set and then sync as described in the plugins instructions page: https://www.getmusicbee.com/addons/plugins/48/ipod-amp-iphone-driver/