All that matters is that you should be able to issue sql to the sqlite embedded library and get back the results.
Freeing you from the overhead of owning (thus inventing and then maintaining) your own file format is almost the entire point of using sqlite in this manner.
This has nothing to do with sqlite. You can have (or not have) gradual saves in any file format. It's a choice that the developers of that app made.
> file format may have braking changes
The sqlite file format is unchanged for 19 years now. A world of features and capabilities have been added since. Don't hold your breath waiting for the sqlite format to change.
Fair enough about the history of it not changing and you can always embed a frozen copy if it does. But this is a pragmatic assumption not a guarantee.