A configuration like that comes from the program using sqlite. Just adding sqlite into a system doesn't set up any data formatting like that. Sqlite itself gives you a blank canvas. And a blank canvas is not much of a data format.

The SQLite data format includes the schema, in plain ASCII. This self-documenting nature makes it an excellent data format, I've taken advantage of it numerous times in making use of SQLite-based application file formats.

SQLite is put forth as a basis for an application file format, and by definition it must be sufficiently flexible to accommodate any application. But by including the schema, it is self-documenting as to what the structure is, which ZIP isn't and can't be. QED.