A database carry the schema, structure, that allow you to validate that you are still having the structure you want.

So do all file formats.

SQLite is both a file and a database, but what I’m saying is that people shouldn’t mess with the file, but the database interface instead.

The same holds for all file formats: don't go around licking random bits in a file, use a client instead.

I have nothing against third party clients, the important thing is keeping the structure.

That's what file format clients are for, and anyone can even roll out their own if they want it.

The facts a DB use the Filesystem behind the scenes, is an implementation details the user shouldn’t be much concerned about, some DB can do without Filesystems.

That's really besides the point. The point is that it doesn't make sense to frame using databases over files as using a higher level client over persisted data.