A lot of the author's reasons have to do with lack of a spec. This topic was brought up by Jeff Atwood (creator of StackOverflow) last year -- http://www.codinghorror.com/blog/2012/10/the-future-of-markd...

I had to build some markdown functionality into a project the other day, and so I googled around to see if there has been any update on this. Didn't find anything official, but a few random comments and blog posts here and there seem to indicate that StackOverflow, Github, and Reddit are working together to come up with a spec.

(Apparently John Gruber has disavowed any responsibility for leading the community in this regard, so now it's up to the big users of markdown to figure something out on their own).