Markdown represents, honestly, the massacre of the art of typography. It is ironic how such an ugly standard clashes with the its inventor's purported love for Apple, a company whose very DNA is about the beauty of layout, fonts, and the visual representation of the written word.
Markdown -> you have been weighed in the balance and found (severely) wanting.
In the case of using markdown for generating web based presentations, your CSS would be responsible for the styling - just like any other web page.
Markdown is just the semantics and content.