PerfectIt does work with 'track changes'. However, markup/tracked changes should not be showing while PerfectIt is running. If you have tracked revisions in your document, you should:
In PerfectIt 5, additionally make sure that 'Revisions Mode' is enabled. To enable revisions mode, go to PerfectIt's 'File' menu and select 'Options'. Then click the 'Revisions mode' tab and tick the box for 'Use revisions mode with tracked changes'. This improves the accuracy when working with tracked changes and ensures that the Fix button works correctly.