The "inserting special characters" one is a bit of a "eh?" for most of us Mac users, I think, since most special characters can be typed using the Option key and the character chooser (which is indeed not very convenient!) is system-wide and should work in a native build of at least the GUI version of Emacs. But, yep -- Markdown and Word aren't the same categories of things. How comfortable your Markdown editing experience is depends on how comfortable your Markdown editor is.

(Also, I wrote a Markdown-to-ePub script, too! Although I don't think anything I've got up online uses it anymore.)