I’ve been referencing the Blueprint doc and the Blog sample file, but niether seem to go into this specific case. What is the recommended best practice?
Your issues.yml would have one or more pages sections (depending on whether or not you want different sections for different statuses) limited to subpages with the issue.yml template.
Then your issue.yml would have one or more pages sections, limited to subpages with the article.yml blueprint.
Finally, you would have the article.yml blueprint with fields for your article.
Since both issues.yml and issue.yml are only containers without any content of their own, you could make your life easy and set them up with a pages preset, similar to the blog example on that page: