I don't know solution for Markdown editor. However if you are using default CKEditor or my CKEditor4, you will be able to apply editor to Extra Question Field. But this solution is required 1 hack.
1. Add either of plugins
2. Hack L31 of qa-wysiwyg-editor-admin-layer.php OR L18 of qa-ckeditor4-admin-layer.php
if (empty($firstrequest) || $firstrequest != 'admin') return;
if (empty($firstrequest) || ($firstrequest != 'admin' && $firstrequest != 'ask')) return;
3. Add "extra?" to "Name list of TEXTAREA tag which applies WYSIWYG editor(separate comma)" option of plugin option panel. "extra?" is field name attribute which you added with my EQF plugin.