This is a very related question: http://question2answer.org/qa/44162 . Read that one first and then read the rest of this post :)
Q2A is able to handle file uploads. Editors generate the HTML for posts that link to the uploaded files. Q2A editor plugins provide the interface for the particular editor to use the already existing Q2A file upload features (backend). The editor should also provide a user interface component (frontend) so that the user is able to add a file so that it can be processed by the backend.
I took a glance at the markdown editor plugin and it seems not to have the backend component so it makes sense it doesn't have the frontend either. Those features should be part of the markdown editor rather than Q2A itself. Maybe Scott, the plugin developer, can shed some light on the roadmap of the plugin and see if those features will or won't be added soon.
Edit: I just noticed someone forked Scott's project on GitHub and added this feature! https://github.com/bvassy/q2a-markdown-editor