Don't markdown files already have a MIME type of text/plain? Isn't that the point of markdown?
It seems interesting in the context of version controlled markdown files written for a particular hosting platform's markdown flavor, but I don't think a specification for identifying the flavor is the solution. This could be no different than any other form of documentation that is generated by a script or framework, but code hosting platforms have decided to make opinionated decisions for a magical UX.