I'm observing that with cleanup: true, running external commands with $I->runShellCommand('php bin/console ...'); isn't working. I'm guessing this is due to the transaction, which prevents external processes to "see" the database contents created/modified by the test. Can you confirm this?
If so, I would suggest to change the recommendation at https://codeception.com/docs/modules/Doctrine to cleanup: false, and show people how to load their fixtures in function _before():
$I->runShellCommand('php bin/console doctrine:fixtures:load --no-interaction --env=test');
IMO the currently recommended way to cleanup after each test doesn't work out, since for some tests it's necessary to disable the transaction (see above) - which ultimately leads to a mess.
So I'm figuring the best approach would be to just reload the fixtures before each test.
What do you think? How do you handle that?