I did find a way, though not as elegant as I would have hoped. I installed the drakkan/sftpgo docker contain to run SFTPGo. I added an extra volume map for "/mnt/user" to "/somepathincontainer" so the container can access the home directories of my Unraid users. From there you can configure SFTPGo users in its webUI, and set their home dir to the container path pointing to their Unraid home dir.
In hindsight, you could just spin up a basic container with CentOS or the like and map the volume as above. Then install sshd_config(5) and configure the chroot dir as normal. You'll still have to setup the user in the container, but chroot should work as its now using the CentOS dir structure and not Unraid's.
Again, not pretty, but '¯\_(ツ)_/¯