Craft CMS HTML Email Template
The "HTML Email Template" option in Settings > Email in the Craft control panel is completely unrelated to the Contact Form plugin.

If you want to change the body of the email that gets sent out, you'll need to write a plugin that listens to the beforeMessageCompile event as documented here: https://github.com/pixelandtonic/ContactForm#the-contactformbeforemessagecompile-event