I guess you could describe aufs as an overlay type thing, but I am not very fluent in any of this stuff, so there may be a better choice.
And yes, I agree that 'mount -a' would have the unintended side effects you describe.
Also, I find that I must manually umount that aufs mount point before the disk can be locked. This is becasue I added all those aufs mount points into /etc/fstab by hand. I am not sure if OMV could have been used to do that. They are below from my fstab, maybe someone can elaborate on how OMV might be able to create them - but I suspect the Union Filesystems plugin lacks that kind of granularity for my use case. /home/sftp is a chroot folder.
# >>> [sftp]
none /home/sftp/outgoing/movies aufs br:/media/41991950-4d12-4475-86b8-ba54ec09323b/multimedia-content-d1/movies 0 0
none /home/sftp/outgoing/music aufs br:/media/41991950-4d12-4475-86b8-ba54ec09323b/multimedia-content-d1/music 0 0
none /home/sftp/outgoing/tv-series aufs br:/media/41991950-4d12-4475-86b8-ba54ec09323b/multimedia-content-d1/tv-series 0 0
none /home/sftp/outgoing/test aufs br:/media/2d02dbfc-9995-4ddd-934a-22265ac7f919/multimedia-content-d3/movies 0 0
# <<< [sftp]