I'm sure you didn't understand that this only happens when you add a related post within a post.
Look at the attached image.. when you click 'add new XY post', there is a popup form like in the image I attached earlier (however, I will attach it again). In THIS form, there are no additional shortcodes. Only default TinyMCE.
Unfortunately there is nothing we can do about this. From what I can see we, the Equation Editor plugin only loads to the editor on the initial page load.
However since the related posts Editors are being loaded dynamically after this then it won't show up. The Equation Editor would need to be constantly listening out for when a new WYSIWYG editor in order for it to add the option to the editor.
The Equation Editor team would need to look at this from their end.