Notwithstanding any other law to the contrary, the department shall have an independent certified public accountant audit the department’s books and accounts for each toll project or system at least annually. The audit shall be conducted in accordance with the requirements of any trust agreement securing bonds issued under Subchapter C that is in effect at the time of the audit. The cost of the audit may be treated as part of the cost of construction or operation of a toll project or system. This section does not affect the ability of a state agency to audit the department’s books and accounts.