All the HTML reporting options display your markup in a normalised form, highlighting valid, deprecated and bogus markup, as well as elements which are misplaced. Note that this is not HTML validation, for which you should use Page Valet. When evaluating against the WCAG at level AA or higher, any invalid or deprecated markup is an automatic fail. Accessibility Warnings are shown according to your selected report options as described in the Help Pages.
The Level 2 report options enable you to prepare and publish Executive Summary reports for management and QA, while the Cleanup options offer a simple facility to remove bogus markup generated by defective authoring and publishing tools.