WPSSO provides HTML meta tags for webpage headers and the Google Structured Data Testing Tool can check these header HTML meta tags, along with Schema and Microdata HTML markup. The Schema and Microdata markup should be included throughout the document's body to identify sections and specific information for Google and other search engines. The addition of Schema and Microdata HTML markup is managed by the WordPress theme templates. Some themes templates may provide actions and filters for various sections of within the templates - that could be used by plugins to add Schema and Microdata - but generally Schema and Microdata markup is hard-coded directly in the templates. To add or modify the HTML markup in this case, you generally have to edit the relevant theme template(s) and/or theme functions.
The Google Structured Data Testing Tool breaks down the analyzed content into several sections. The hAtom section reflects the Schema and Microdata markup found on the webpage, and does not include any information from HTML meta tags. You'll find most of the HTML meta tags added by WPSSO in the rdfa-node / property section.