Disabling Generate automatic URL alias is not possible with configuration, this needs to be done with code.
In hook_form_alter we call
/**
* Implements hook_form_alter().
*/
function myModule_form_alter(&$form, &$form_state, $form_id) {
// disable auto generating of URLs with pathauto
if ($form['#entity_type'] == "node"){
$form['#after_build'][] = 'myModule_after_build';
}
and then we create that after build myModule_after_build
/**
* Custom after build function
*/
function myModule_after_build($form, &$form_state) {
// Unchecks Generate automatic URL alias
$form['path']['pathauto']['#checked'] = FALSE;
return $form;
}