A more relevant example: this is how .docx files work, for very much the same reasons (one XML file at the root, and then a bunch of referenced resources.)
.zip seems to be the universal 'combine some stuff in a single file' format, probably because it is old enough to be guaranteed patent free (OTOH: http://broadcast.oreilly.com/2010/06/is-zip-in-the-public-do... and http://www.pkware.com/support/zip-app-note. http://www.pkware.com/documents/casestudies/APPNOTE.TXT only mentions encryption and patching as patented)
One could even imagine padding files in the archive so there's some leeway in growing the compressed files, it'd likely depend on the format expression.
Any performance benefits sqlite might have are easily outweighed by the ease of interacting with the zip-based format.
It also has the advantage that if you extract the zip you can now access whatever pieces are inside as separate files even by tools that don't understand the containing format. (eg a bunch of jpg/png inside the zip are perfectly viewable in any image viewer). Trying to do the same with SQLite is problematic as you have to write queries to grab the blobs and then dump them to disk.
Where SQLite as a format does shine is if you need to keep historical information such as an undo/redo log. That makes it good for an application format, but not for an interchange format.