Pretty much as the title says. Is there a reason I should favor Markdown over HTML in posts to Stack Exchange sites?
The only advantage of Markdown in comments is that less characters are used. In fact, for sites like this I don't see any point in using Markdown; what would be much more useful is a WYSIWYG editor, because the posts are never viewed in raw text format, except in editing but a WYSIWYG would solve that.
and I'm guessing that once you've posted the Markdown is converted into HTML and the exact markdown you used is lost?
While Markdown can make sense for programmer sites, sites like Cooking are less likely to know it and more likely to know BBCode or something that most forums use at least.