TYPO3 Core

Good catch. The "sql logging" is done manually by each upgrade wizard, so its not tracking the SQL executions on the source.

e.g:
$res = $GLOBALS['TYPO3_DB']->exec_UPDATEquery('pages', 'doktype=2', $updateArray);
$dbQueries[] = str_replace(chr(10), ' ', $GLOBALS['TYPO3_DB']->debug_lastBuiltQuery);

...

Since the SQL creation through the EM happens in "some nested down" methods, it is not so easy to get to that information.

Best solution would be to add a method on t3lib_db to "startTrackingQueries" (only INSERT/DELETE/REPLACE) and "stopTrackingQueries" where the wizard caller can later simply call "fetchTrackedQueries" or something like this. Then we would get all queries that modified something (which went through t3lib_db at least). But this also has to consider DBAL etc.. Probably something interesting for 4.6.