Don't think anyone could tell you if size of those items is 'too high'! Much depends upon what teachers are doing in courses - obviously, that won't be the same on any two systems.
As far as expanding space on a VM system. To the best of my knowledge, while it's easy to tell the VM to allocate more space, Linux virtual systems do not automagically see the expanded space and use it. One has to tell the linux guest system to use it ... ie, 'grow'. See your distro's docs.
Seems I re-call that the emptying of the trashdir is from cron and the default setting is to empty in 4 days. So it's possible that the trashdir would grow overnight. Have you tried running the cron job via command line in admin/cli/cron.php? repeatedly? (ie, not just once).
See your autobackup is set to 1 and to save in the course area ... well, that will save the most recent backup to filedir/whereever/ and it should move former backups to trashdir for emptying later. Thus trashdir would grow.
To be honest, think concentrating on expanding space is priority one. Get that job done first and these other issues may disappear.
How much space? At least double what you've allocated ... more would be better (if one has space available in the VM environment).
Since you are running Linux, one could 'watch' the process in two terminal session screens. In one terminal session, logged on as root user, go to /moodledata/temp/backup/
Then issue 'watch ls -lR'. That will show you realtime activity in that directory as courses are run through the backup process (go to one of those failed backup courses and run the backup manually from the course menu in a browser).
In the other terminal session, logged on as root user, go to /moodledata/trashdir and issue the same command.
You may/may not see any activity in the trashdir, but suspect you will considering backup settings.
Sounds like a lot of trouble, but one needs to get a handle on how the new file system works and can't think of a better way than observing behavior in real time.
'spirit of sharing', Ken