I agree with (basically) all of this, the larger point. I'll note that I said "or"... ;-) (CYA)
I'm not sure what the "right" solution looks like, perhaps a directory of TOML or JSON files. Perhaps the aforementioned + executable shell scripts with predictable naming? handwave handwave as long as it's "UNIXy". (consist of easy to edit text & not invent a new anything & be composed of pieces which do one thing well)
> text files or symlinks for configuration and text files for logging.
Systemd gets this right and arguably pushed the whole ecosystem in this direction. The old rc scripts could barely be considered a text file and symlink configuration system — they were a pile of text files containing a miserable combination of code and configuration mixed together, along with a very simple configuration (this service is enabled in these runlevels, more or less) that got translated, hopefully correctly, into symlinks. Of course, nothing really kept the symlink farm consistent with itself or anything else except a pile of additional scripts associated with packages that tried and usually succeeded.