Many programs use fopen(), fread(), and fwrite() to create and manage files of data in home-grown formats. SQLite works particularly well as a replacement for these ad hoc data files. Contrary to intuition, SQLite can be faster than the filesystem for reading and writing content to disk.
Comments
https://www.sqlite.org/whentouse.html
That quotation is about a SQLite file db being a better choice than multiple ad-hoc binary files. It’s not saying whether SQLite uses direct IO.