I was thinking of the Use Case where you take some existing Markdown. Apple is going to use it in their Notes app, for example, so it might become even more popular.

I also have md on Github that I might want to use.

Oh, I wouldn't Markdown that represents real documents to produce anything useful, so I just automatically skipped that possibility.

If you've got a real document that produces a non-trivial graph when you render its headers this way, you've probably got yourself a really, really poorly written document. Written text needs to have been serialized somehow, and as a side effect, you'll make the graphviz view of the document pathologically uninteresting. Conventional outline views are much better suited for written text.