You have the ability to disable a specific configuration handlers in case you need to. This could be useful if you want to deal with a specific component in a different way (features for example) or just simply avoid the dependencies detection for it.
For example, the permissions configuration is a dependency for several other components and are controlled by the PermissionConfiguration class.

You can disable a specific configurations handler by following this example:
Create a module and implement hook_configuration_handlers_alter(), the following code disables permissions configuration support.

/**
 * Implements hook_configuration_handlers_alter().
 *
 * @see configuration_configuration_handlers().
 */
function yourmodule_configuration_handlers_alter(&$handlers) {
   // We don't want to track permissions with Configuration Management.
  unset($handlers['permission']);
}