I'd separate backing up the VMs from backing up the actual data. For the Proxmox side, I'd use PBS if you can. It's honestly one of the best parts of the Proxmox ecosystem. Incremental, deduplicated backups, built-in verification, retention policies, and restores are incredibly straightforward. If your backup server has to stay on Ubuntu, you can still run PBS in a VM or LXC, or even on a small dedicated machine. For the TrueNAS data, I'd use restic or borg to back up the datasets themselves. Both are excellent, but I'd lean slightly towards restic because I find it a bit simpler to manage, and it supports encrypted, deduplicated backups to a wide range of storage backends. My biggest recommendation is not to rely solely on VM-level backups. If your Docker containers are configured properly (Compose files, configs, and persistent volumes), make sure you're backing up the persistent data as well. Restoring a VM is great, but restoring just the data you actually care about is even better.

You can run Proxmox backup server on bare metal on the same machine as Proxmox. You can also run it in a VM. It’s by far the best solution for backing up VMs. Nothing else will get close in terms of data deduplication and minimizing storage requirements. You can use it to back up the Proxmox hosts too. Then use borg/restic/whatever to backup the datastore offsite.