There's a "type" field in the spec, defined as: "The UTI of the text.* file. E.g. set to net.daringfireball.markdown for Markdown. This field should default to net.daringfireball.markdown to be backwards-compatible with version 1."
So it's whatever you care to specify. Doesn't have to be Markdown at all. It looks like it'd be completely valid to use this as a way to bundle up a webpage with all associated images and scripts, for instance.