The answer is that you cannot.

The only workaround I can think of it to add an `account` metadata:

    $query = new EntityFieldQuery;
    $result = $query
      ->entityCondition('entity_type', 'node')
      ->entityCondition('bundle', 'foo')
      ->fieldCondition('custom_id', 'value', $custom_id)
      ->addMetaData('account', user_load(1))
      ->execute();

EDIT: a `DANGEROUS_ACCESS_CHECK_OPT_OUT` option has been added as part of the Drupal 7.15 security release.