This feature was prototyped for MarkdownPad 2's initial release, but after working with many users I learned that their main goal wasn't to modify the entire HTML template; instead, most actually wanted to simply insert content into the
<head> section of the document.
To make this possible, I added a "Custom HTML Head Content" editor under Tools → Options → Advanced tab → HTML Head Editor button.
Since adding the
<head> editor, I have not received any additional requests for a feature of this nature. It's still on my list, but has a lower priority than it originally had.
Are you seeking a full HTML template editor? If so, can you explain the use case? It helps me get a better understanding of the requirements.