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In regards to full system backups, there's no real need to back up the OS itself. Canonical will give you a clean Ubuntu install if you ask then nice enough, after all. Personally, the risk of having to spend an afternoon reconfiguring my system isn't that big a deal compared to the storage and time needed to back up an entire image.
I know systems generate a lot of "cruft" in terms of instslled programs and tweaked configurations over time which can be hard to keep track of and remember. But imo that should be avoided at all costs because it leads to compatibility and security issues.
For backing up databases, there's scripts like automysqlbackup and pg_dump which will export a database to an sql file which can be easily backed up without worrying about copying a broken file.
I actually recently set up borgmatic earlier today and I'd recommend it except for the fact that you seem to be using Docker, and I'm not sure how best to backup containers.
I usually also backup the etc directory so if I had an issue I would at least have the config files from the old setup. This has already saved me a few times when I have really messed up configuration files.
Yeah, I keep everything as simple as possible. Everything is containerized, and all the configs live in one directory and they store their data on my RAID. I don't need to go track down configs across the system, and adding a new service doesn't require any backup config so no risk of forgetting something.
Docker is simple. You map directories in the container to directories on your host, so you put the important data where it'll get backed up and the less important data (e.g. logs) where it won't.