Have you searched Moodle plugins?
https://moodle.org/plugins/index.php?q=backup
https://moodle.org/plugins/index.php?q=restore
Does visiting a course and pretending to restore show you what you seek?
As far as extracting just .mbz files from moodledata/filedir/ individually or in mass ... yes it's possible, but it would involve db query of mdl_files table to find .mbz files (names and locations - location is the contenthash) then copying those .mbz files to another file system location so they can be seen by Moodle interface for restoring. No GUI/plugin for that but I do have some cli scripts (a combo of bash shell scripts and .php files that uses xmlint) that currently extracts files from a .mbz file which you could adjust to work with server/moodledata/filedir/ ...
Moosh might have something useful for ya:
https://moosh-online.com/commands/
I imagine this could be massive ... depending. One would want to have plenty of drive space available me thinks.
'SoS', Ken