I run unbound alongside pihole for extra privacy and I keep my unbound config in git. I have gitea set up to push out new unbound configs every time there’s a git push.

This would be a great use case for ZFS. You can use dataset replication to sync the data. I’ve been very happy with TrueNAS but I think it only became recently available for the Raspberry Pi so not sure I would recommend it but I think you could use ZFS. You can use RAID-Z too if you multiple drives. The only limitation you might encounter is memory since ZFS is a bit of a hog. On the plus side though, ZFS should protect against bitrot if you’re worried about that.

I’m not familiar with paperless but do you have PAPERLESS_BIND_ADDR set? maybe try to set it to 0.0.0.0

If you go the ZFS route, you could check out syncoid.

Some other tools that might be worth considering (that aren’t related to ZFS) are borg and restic.

Hope that helps.