One thing that is hacky/a problem with the app is that I wanted to be able to hash tag notes and have the hashtags a different color. Also very soon i'd like to add the ability to highlight text. It's pretty hard to do that smoothly even with the contenteditable attribute.
I decided on a transparent textarea over a div and I sync and transform the content. It is a bit clunky as you say but I anticipate it will get better.