Hey @Jamographer,
The theme has no connection with Yoast SEO nor other SEO plugins because they could not read the site’s code. They only could read the content and the content can be made using page builders like Cornerstone or Pro’s Content Builder. It can also be made by other page builders like Visual Composer.
It is the Content Analysis of Yoast SEO that is not working well or needs fine tuning to read Cornerstone’s content properly. With regards to compatibility with Cornerstone, Yoast SEO is compatible. There are just certain conditions where the content analysis fails like mixing Classic and v2 Elements in a page or not analyzing.
In a perfect world, it’s best for all SEO plugins to analyze the output of page builders in general. But, that’s currently not the case. Continual enhancements are needed to be made.
Also, Yoast SEO works best analyzing HTML written directly in the WordPress Content area or Text Editor. The main use for that is for writing blog posts. Most users don’t use page builders for writing posts.
Pages, especially pages built with page builders are usually used for landing pages. Landing pages are usually not optimized for SEO because they’re rather used for marketing like sharing the page on social media sites. But, the said pages can still be read by Google or any search engine crawler therefore they still can be optimized if needed.
Hope that information is useful.