We are using a theme that is 100% custom and rarely use the WordPress default editor, except for blog posts. The issue is that the SEO Checkup report only contains data for the home page.
The other thing I noticed is that if the content on a page is in the page template, or if it's a custom field, the plugin does not make any recommendations. It seems to only scan content edited in the default WordPress editor.
The only way I have found to see individual recommendations is to actually go to each page in the Admin one by one.