IMHO this (having a variable number of files containing the data, depending on your configuration) is the only real design quirks of this technology.
If you're using it as a standalone file format you presumably shouldn't leave .sqlite files with associated wal files lying around in places where users are going to get confused by them, either by sticking to the rollback journal mode or by using some other method
Also, a scheduled backup process might come along at any moment and non-atomically copy the database file and any -journal or -wal files.
Ideally, user visible files should survive copying at random points in time without corruption and without losing too much recent data.
Having read "How To Corrupt An SQLite Database File"[1], I'm still not quite sure how to achieve this.
I know reading the manual isn't very common and people are lazy, but getting burned can be a useful and necessary lesson.