The LE settings add-on backs up only /storage/.cache|.config|.kodi .. and nothing else; the design assumption is that covers all the essential config items to restore to another device, but not media which is normally too large to duplicate/store. The backup files are saved to /storage/backup if you want to move them off-box or delete them to free up space.
The backup addon in the Kodi repo will be more flexible .. but is someone else's problem to educate and support on.
If you have other Linux devices you can save to, installing the network-tools addon and using rsync from a cron task is probably the easiest approach to an automated backup.