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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();