Mailmate translates Markdown to HTML, then sends the e-mail.
Drafts can translate the Markdown to HTML and then send via Mail Assistant.
I’m a Mailmate user myself as I prefer composing in Markdown; but really the difference is what app handles the conversion to HTML. So the chances are for practical intents, it does not matter that Mailmate accepts Markdown and Mail Assistant does not. Your input is Markdown, the resulting output is an HTML e-mail.
However, if you truly **need** the content to go via Mailmate, then use a script action step to trigger a shell command that utilises Mailmate’s command line interface, eMate. That would do what you need.
Hope that helps.