We could debate many things about this!
Understanding the changes to file system and why those changes were implemented depends upon past experience with series 1 of Moodle. Back in 1.9.x, if a teacher who taught 2 or more courses had a PDF file they desired to have linked in all of their courses, that PDF would have to uploaded to each course. Moodledata had course ID directories and that's where all files (as well as backups for that course) were stored ... by humanly re-cognizable names.
In the new file system, that one PDF file could be used in multiple courses ... thus saving space and time and effort by a teacher.
Something you need to explore ... login as a teacher and backup one of that teachers courses. Where does that backup show? Now if things have not changed, that backup will go to the teachers private files area ... moodle admin level users can't see that area via GUI.
I do agree that backups *could* be handled differently but that depends ... the question then becomes (as you had mentioned, privacy/ownership etc. is more of an issue in Academia (individual professors/teachers) than it is in a Corp site - when it comes to files/backups, etc.). It's a problem for the admins ... but not the teachers. Then there is the difference between a corp moodle and one for Academia - I do admin a couple of K12 sites and several Corp sites - and have had access to small University/College sites for 'jobs'. Each have a different take on things in general.
I use command line scripts in moodlecode/admin/cli/ for backing up courses ... one reason, web service taken out of the loop for very large courses ... a team taught multimedia course with audio/video files the troublesome course - 130Gig is large and got to the point where it couldn't be backed up via GUI ... let alone restored should something go south with that course.
And we do have to understand ... me included ... that Moodle tries very hard to be one-size fits all ... if not using special plugins.
Sooooo ---- ???? I have *no* 'one-size-fits all' answers! :\ Some, however, will tout that's 'a plus' for moodle ... flexibility ... but not without development of plugins to accomplish.
'spirit of sharing', Ken