What makes the most sense for you to do is not to try to make covers themselves specifically show all your articles, but to make the archive page for your “Issues” taxonomy include both the cover and the articles. This is better both conceptually and practically.
To to do it, I’ll assume your issues taxonomy has the slug “issues”. Then, what you should do is create in your theme a file called taxonomy-issues.php (I’d start by just duplicating your existing archives.php and renaming it), this will then be used by WordPress as the default view for all issues taxonomy archives. (If you’re curious, the source of that wizardry is the WordPress Template Hierarchy.) So that if a user goes to //yoursite.com/issues/1, they’ll see a page generated by taxonomies-issues.php.
With that set up you can then customize your taxonomy-issues template to include pulling in other post types like the cover. The most obvious thing to do would be to have your cover posts use the same slug as your issue, so that (given my example) your first cover would just have a slug of 1, or 1-cover, or some other obvious format so you can easy pull it into that template programmatically by using something like (or literally) get_page_by_path().