When you set autoplay to OFF in the Drupal UI, the embedded URL shows it as true

This is because the check for adding 'autoplay', 'enablejsapi', 'loop', and 'modestbranding' to the src url only check of the option is set, they do not check the value of the option, and if it is set to either true or false, the URL sets it to true.

 if (isset($variables['options'][$option])) {
   $query[$option] = 1;
 }

should be

  if (isset($variables['options'][$option]) && $variables['options'][$option]) {
    $query[$option] = 1;
  }