I think Virtualmin's Set-User-Quota inside the User Editor (not Webmin) does set quota in the wrong place if the home of the users is not on /.
This output is shown after setting a quota for user du@hoi.
Disk quotas for user du@hoi (uid 1059):
Filesystem blocks soft hard inodes soft hard
/dev/vda1 0 2048 2048 0 0 0
/dev/vdc 80 0 0 21 0 0
In this example my Virtualmin HOME is on /dev/vdc, mounted on /media/storage, while /dev/vda1 is on /.
Doing it manually via the Webmin module works.
Virtualmin knows that the Maildir is on: /media/storage/vm_userbase/hoi/homes/du/Maildir, as seen in the User-Edit-Mailbox Panel. This also is the case even if the Unix-User-HOME-Base is set to /media/storage/vm_userbase, too.
Webmin version 1.910
Usermin version 1.751
Virtualmin version 6.06-2
Best regards Manu