Thanks Jason. I wondered if I could just change that line but wasn't sure. I also didn't realize that the doctype only affected the full screen editing.
What I was trying to do is constrain the html generated when a user enters text and formatting into the editor, to be HTML5 valid. The pages that the entered text is displayed on is an HTML5 page but the code generated doesn't validate and it bothers my client. For example, tables include spacing, padding and border attributes. These are all handled by CSS in HTML5. I assume there isn't any control over that at this time.