For me the point of using Docker is that it's a unifies configuration and backups, and makes installation easier.

I can easily see which directories or files to back up, and it's fairly explicit which knobs I've tweaked or config files I've changed, regardless of what stack the app relies on.

It's also makes it much easier to roll back a version. Just take zfs snapshots of relevant directories before pulling new image, if it goes south just roll back snapshots and use the old image.