It has SO MANY advantages over every other solution. It can do the "just a bundle of files" thing, but it can also do all this rich data as well. And unlike most "just a bundle of files" formats, it's incrementally updatable, it's so good. We're using this in production right now and couldn't be happier with it, wouldn't dream of using anything else at this point.
One notable application that uses SQLite for this is Audacity: all the stuff you record is streamed into a SQLite database (the project file). This is a huge reason why Audacity is so good for recording long sessions, and why it's so resilient against crashes and failures.