I resolved this specific problem by changing the configuration. I now have a single 318Gb LVM volume group running on top of a RAID1 device on a pair of physical drives. A small second RAID1 on the same pair is mounted as /boot (non-LVM).
The LVM volume group has two logical drives for the host system: one as swap and the other with 20G at /root. This part of the install is pretty much static; quota is not installed. The rest of the volume group space hosts several KVM instances. Each KVM was created on separate logical volumes of 20 - 40 Gb apiece mounted at (root) ~/vm1, ~/vm2, ...
One of them (an ISPConfig webserver) is now running quota without a problem, the other (a document management install) will have it shortly. If there is a problem I'll post it here.
All of this is to say that the original problem remains intact as far as I know, but at this point I won't be going back to fix it.