$maintenance->setConfig( ConfigFactory::getDefaultInstance()->makeConfig( 'main' ) );
$maintenance->finalSetup();
// Some last includes
require_once "$IP/includes/Setup.php";

We now load extensions from the top of Setup.php, meaning that if they want to register their config types, it's too late. AFAICT we cannot move up Setup.php to before finalSetup() because it needs to run before extension functions. So I'm thinking we should just call Maintenance::setConfig() *after* Setup.php runs and say that finalSetup has to use globals for now.