The Comptroller may direct the units of the State government to use the method that the Comptroller sets for: keeping books and accounts; adopting uniform systems of accounting; or making reports. Except as provided in paragraph (2) of this subsection, the Comptroller shall require a unit of the State government to comply with each recommendation of the Legislative Auditor in an audit report on the unit concerning: its record keeping; its use of a uniform system of accounting; and its submission of reports. The Comptroller may waive compliance with a recommendation of the Legislative Auditor if the unit satisfies the Comptroller that the recommendation should not be carried out. The Comptroller shall report to the Joint Audit and Evaluation Committee on actions under this subsection. The report shall include the reasons for waiving compliance with a recommendation of the Legislative Auditor.