Drupal 7, MySQL, InnoDB, and transactions
The constructor for the DatabaseConnection_mysql class, has this code and comment:

public function __construct(array $connection_options = array()) {
  // This driver defaults to transaction support, except if explicitly passed FALSE.
  $this-&gt;transactionSupport = !isset($connection_options['transactions']) ||
    ($connection_options['transactions'] !== FALSE);


In addition, there is support and workaround for the MySQL implementation of transactions (including no proper support for DDL transactions).

This suggests that the documentation in the settings file is incorrect.