In general I think I just don't like the idea of one URL being able to return different content. Forces me to think about what each system I give that URL to may be sending in content negotiation headers. Would rather the HTML is returned and alternatives listed in HTML head.

But for HTML and Markdown in particular, there's been so much useful work done in the semantic HTML space and microformats, that I don't know why anyone interested in this wouldn't just improve their HTML markup and leave it to the agent to do the rest. Convert to markdown or extract the useful HTML before handing it to model.