You are right that storing notes as individual text files in the file system doesn't guarantee safe read-write access. But I don't agree that these design decisions are orthogonal.

How would you design a system that uses SQLite as primary storage for notes (rather than just as a search index or metadata store) while still letting people edit those notes in any text editor, sync via any cloud and make them accessible to any AI or other third party software that knows how to use a file system?

Exporting and re-importing every single time you want to edit a note is impractical for tech folks and impossible for regular users.

I can imagine a partial solution using FUSE, FileProvider and whatever the respective file system abstractions are on other platforms. But that would be a huge amount of work.