This type of template is currently available only for the server version.
Creating a markdown template
Navigating to templates tab, you will find an action under Create - Markdown template.
Clicking on Markdown template, you are brought to the markdown template builder.
Here JQL section is added in textual format. If clicked on, edit & delete actions appear on screen. The JQL section pop-up is exactly same as that of other template builders.
A sample markdown can be generated by clicking on preview & then selecting a version. In case of markdown, a view action appears that allows you to view the raw markdown or resulting html.