checks whether a html template for sending the activation email exists. If yes, it uses a multipart email and the user receives a nicely formatted HTML mail. If no .html template exists, it just uses the plaintext variant.
For anyone else who comes looking at this, I found a solution that someone posted.
The solution was to just override the default RegistrationProfile to send html emails, see here for the code: http://stackoverflow.com/a/5128916/485048