I haven't dug into this too much, but I have seen mention of using overlay2 for lxcs on proxmox. If that was available would you still prefer VMs?
Here's one post I just found talking about the availability of it: https://forum.proxmox.com/threads/lxc-zfs-docker-overlay2-driver.122621/
I use double killer on Windows and rmlint on Linux. With rmlint you can use tagged directories and tell it to keep the tagged and only match against the tagged. It has a lot of options, but no GUI.