> I am guessing this let's you set coordinates for how to lay the canvas out but this is exactly why I'd never use it.

You wouldn't like a text editor that automatically rearranges source code or sections of a document without you having a say in it, and for the same reason I find manual layout for this graph feature absolutely necessary. And beside that it's very likely you'd want some other metadata that just have no place in standard Markdown. Maybe a viable alternative would have been generating graphviz dot code and embedding it in Markdown code blocks, which would make it compatible with other tools as well - that could still be added via plugins.