For the most part it's either epub or mobi at this point in the ebook game, with the rare occasional pdf. Epub and mobi are essentially interchangeable thanks to Calibre, and if you need PDF then you probably need more complex formatting than a Markdownesque language can provide.
Converting from Word is a problem, but that's for different reasons: 1) authors (understandably) have no idea how to typeset, so each author has their own special bizarre style that's almost always wrong, 2) the HTML produced by Word is a hideous wreck no matter how you slice it, and 3) each different version of Word produces wildly different, but equally monstrous, HTML.
Sadly the word processing game has been won by Word. 99% of non-techie authors will use Word (or maybe Scrivener) to write their novel and it's tough to convince them to learn a formatting language when they can just press 'bold' on the toolbar.
In either case we already have a format to be invisibly used by writing software: HTML/CSS. It's the underlying language for epub and mobi, it's well understood and easily learned, it was specifically designed for book-like documents (and not web apps funnily enough), and programs already export in that format. The problem is that some programs (like Sigil) do a better job of exporting than others (like Word).
Things like TOCs can be handled by using an open, easily-editable format like epub as a base format, then using Calibre to invisibly compile to different formats. Calibre does a flawless job 99% of the time.
Edit: My creds are that I run one of the largest writing communities online, briefly ran an online ebook conversion service, and have composed and published ebooks myself.