First of all, I'll show the conclusion. Never use LaTeX via Markdown to make a presentation slide with Beamer.
I have too many reasons why you should not use it to write here. I spent all a day with it, and the only one thing I found was that it was a never ending maze.
Sure, Markdown syntax provides us to simple notation. It may make us happy. But, as a practical matter, it does not help us without we write wrappers for each something forever.