“When your SQLite database is kept in S3, each write suddenly becomes a total overwrite of the entire database.”
S3 has two core calls against the five of the unix file API. The missing piece is partial overwrite, and every database from Postgres to SQLite writes in 4 or 8 kilobyte pages. S3 also has no rename, so a move is a copy plus a delete in linear time, and listing is slower than a slow local disk. Calling it a filesystem sells a lot of S3 and breaks a lot of software.