> but most usage of sqlite is not as an application file format,

This is exactly the OTHER way around. Most usages of SQLite are as an application file format. Firefox stores bookmarks, history, cookies in SQLite files in the profiles folder. Messaging apps (WhatsApp, Signal, etc. use SQLite for chat history). macOS and Windows use SQLite in various subsystems, ex: Spotlight metadata, application cache. Mobile apps use SQLite heavily. And probably ten thousand other cases as a file format if I bother to look up more.