I think it would be good to have both Markdown and Birch format packaged together in the TextBundle format. This was requested here as well: http://support.foldingtext.com/t/textbundle-support/480
This way, upon saving a Birch version and a Markdown version is can be saved in the bundle. Then other programs that support TextBundle (Marked 2, Ulysses, and Highlights) will be able to directly open the TextBundle and display it. When Birch opens and sees the Birch version with a different date, it could import changes to the markdown version.
I use Marked 2 for printing all my Markdown files. Currently, trying to translate a Birch to Markdown then open in Marked 2 is an extra step. With the current translator, I have to run through a TextSoap Cleaner to get the right formatting (The AppleScript puts a ‘-’ on every line. That is due to Birch only doing unordered outlines right now. All of my outlines are line numbered). That makes it two extra steps, which is not ideal.
Just a thought!