When deploying changes to a Drupal environment, you should be running database updates (e.g. drush updb, or through update.php) first, and only then import new configuration. The reason for this is that update hooks may want to update configuration, which will fail if that configuration is already structured in the new format (you can't do without updates either; update hooks don't just deal with configuration, but may also need to change the database schema and do associated data migrations). So, there really is no discussion; updates first, config import second. But sometimes, you need...