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What is your system backup solution like? Having it separated seems convenient for that since you can just back up the vm storage somewhere I'm guessing?
Not OP, but similar setup (Proxmox with docker on a VM). The VM (plus a few LXCs) are backed up daily using the backup built into Proxmox, and those backups are mirrored to the cloud with rclone.
Proxmox Backup Server: Incremental de-duplicateed image backups of the whole VM, with possibility of individual file restore. It's like magic
For the legacy bare metal system I have rsnapshots of the data folder (set it up ages ago, and never changed it)
An nginx LXC container has a single static backup of the container, with the nginx config file stored in a git repo