I wonder why VFMD (http://vfmd.org) isn't the choice among people picking a Markdown specification or parser? Well specified, unambiguous, easily extensible, with a reference implementation, open-source. I'd imagine it could be at least mentioned in the RFC?
Basically a small group of people worked in private for years while there were public community efforts, including a W3C gorup, to do the same. None of the disparate efforts coalesced into a unified front, so the simple answer is that projects advocated for whatever spec their developers backed. The community is fractured.
