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I have a shell script that handles all the quircks. I run it every few weeks. It does a btrfs snapshot so I can go back in case something is wrong, and after it updates Docker and Podman to the latest label.
For services not containized I have some automation to fetch the last version from internet (for example some home assistant addons that are just js files).
For the updates that are more difficult to script (or just not worth because they are very infrequent) I have a script that compares the running version with what published on their website and warns me I have a manual update.
Since most of the projecs I host have a gitub page it is relatively simple to write reusable code to do this stuff.
In general I don't trust automatic updates, there are seldom issues but they can be annoying to fix. So I just prefer to updates by hand whenever I have a few minutes free and I know I have direct access to the server in case the connection drops.