No, not as Bike’s most native file format. I wanted HTML because I want (and eventually plugins too) to be able to add arbitrary metadata to the format. Also I think that HTML is likely to be more readable in 50 years (with formatting, etc) than Markdown.
But I do expect to eventually add support for Markdown, much as I now support OPML and Plain text formats. I don’t know exactly how it will work, bold text will likely be encoded as Markdown. bold formatting… but other outline data (such as persistent unique id for each row) isn’t likely to get saved. Anyway, this is something that I do expect to add, but no timeline other then it’s not what I’m working on now or next.