Instead of scanning the entire filesystem, could the virtual server owner not be allowed to specify one or more paths, such as /mnt/cbsvolume01/username, which could also be added to the users quota?
Cloud block storage is almost universally available at low cost and a Virtualmin admin would benefit much if there was wider and seamless support for it: seamless as in, for example, when invoking fix files and permissions, the same routine which is run on /home/username could also automatically be run on /mnt/cbsvolume01/username