Why not SQLite? You get an efficient file format, and can easily add metadata to each file. That is how the Geopackage format works for storing tile caches for mapping data. There are often millions of small files that don't work well on a file system. I think there is even a standard for storing directory structures on SQLite.
SQLite is one of the options evaluated in the article. I haven't considered it because I feel that it's a proprietary format, and also because I haven't read up on its improvements in the past ~decade. My view is still that SQLite corrupts easily because people were treating it like a proper database and doing multithreaded reading/writing, but in reality it's a different thing that doesn't quite work that way.
