Your initial belief on this was entirely reasonable given what the doc page and sqldiff's --help output said. The doc page has been clarified to emphasize that the (usual) comparison is on content and to note the limited effect of the --schema option. The sqldiff utility has been modified to make it possible to compare schema among databases more completely, via the option:<code> --table sqlite_schema </code>. These changes are available now in the SQLite code and doc repositories. They should be conveniently available at the next release.