If you edit anything in a template outside of a Marketo Element or Module (defined here: https://docs.marketo.com/display/DOCS/Email+Template+Syntax ), it will break the template from the email. At that point, modules that are currently in the email will still be there, but you won't be able to insert new modules (since there is no template to pull from anymore). You can certainly clone our Marketo Starter Templates, make any changes you need to, and then start creating emails from them. That will work fine.
Also, our templates are in the process of being updated right now. So, you'll be able to just use the Starter Templates with local variables once that hits your instance (within 24 hrs is my estimate).
Great news! Thanks Justin!