It’s proven several times over that it’s the correct approach. Abstractions (formerly Google photos, currently Immich) should just be built on top - but these proprietary databases are only for convenience.
For work, I’m having the same experience as the author and everything is just markdown and csv files for Claude Code (for research and document writing).
Ostensibly, things like MacOS Spotlight can bring real utility and value to the file system, and extended attributes through the sidecar indexing, etc. But Spotlight is infamous for its unreliability.
The other issue with file systems is simply that the user (potentially) has "direct access" to them, in that they can readily move files in and up and around whimsically. The "structure" is laid bare for them to potentially interfere with, or, such as the case with the extended attributes, drag a file to a USB fob, and then copy it back -- inadvertently removing those attributes.
And thats how we end up with everything being stuffed into a SQLite DB.