> If they had direct evidence that some author's instructions failed to ask for the case study to be fictionalized, I think they would have specifically said that.

Which they do. They specifically say that. “Neither the instructions for authors from 2010 — when Koren and his coauthor Michael Rieder would have written their article — nor the linked list of article types — state the cases are fictionalized, or fictional.”

“An archived version from September stated, ‘Each highlight is a teaching tool that presents a short clinical example, from one of the studies or one-time surveys,’ with no mention of fiction.”

These are direct quotes from the article. The exact kind you are asking for. With inline links to the archived documents. And yes it is very definitive.

> I'm pretty sure what happened here is that:

No need to speculate. Just read the article.

> 1) The journal always asked for […] fictionalized case studies.

This is false. As evidenced by the article.