Yes, it's a weird point to make. The main thing is that most systems that allow rich text editing do not store the result as markdown (because it's lossy), and instead store html/json.

Also

1. We can do the reverse. We can store the html/json and give you markdown. (We still only store markdown though.)
2. For folks that edit entirely in WYSIWYG, we still store it as markdown.
3. We were limited to pretty simple markdown syntax extensions before because anything crazy novel wouldn't have been accessible and therefore not worth developing. (e.g. you're the only one to use your ToC extension.)