Change the base directory of a backup?

I don’t think that’s possible, but others have expressed interest in adding ZFS snapshot support to Duplicati.

Here is an improvement filed on Github: ZFS Periodic Snapshot integration · Issue #3862 · duplicati/duplicati · GitHub

And there are some threads in this forum where it’s been discussed before, such as this one: Any plans to support snapshots on the modern Filesystems (ZFS et. al)?