The article is basically entirely an answer to that question. The third sentence in particular is: The performance difference arises (we believe) because when

The article is basically entirely an answer to that question. The third sentence in particular is: The performance difference arises (we believe) because when working from an SQLite database, the open() and close() system calls are invoked only once, whereas open() and close() are invoked once for each blob when using blobs stored in individual files. It appears that the overhead of calling open() and close() is greater than the overhead of using the database. The size reduction arises from the fact that individual files are padded out to the next multiple of the filesystem block size, whereas the blobs are packed more tightly into an SQLite database.