I sometimes use a Markdown to BBCode converter. Assuming you're using Github-flavored Markdown, this converter
could work nicely.
You should report your issues with formatting in the "Site feedback" sub forums to help the Handmade Network team improve the site.
The old team was early in the process of switching from BBCode to Markdown, but we never got around to it. Bumping this request to the new team at Site Feedback
would move the needle I think (we've seen Ben do some nice updates / features recently!)