It is, but unless you're doing it all on your own, writing a novel is also about working with editors and typesetters. (Or formatters, or whatever you want to call the typesetter equivalent for an ebook.) In my experience, at least in the fiction world, these folks are going to expect you to be using Microsoft Word, and you'd better have a tool that can generate Word-compatible files formatted to the industry standard -- and that supports Word-compatible comments and revision tracking well enough to "round trip" documents transparently.

I'm a big fan of open data formats and plain text markup, and I write a lot of fiction in Markdown. I love this notion in principle. But I suspect it's a lot easier to put into practice when everyone involved in your book's production is down with your toolchain -- which may mean everyone involved in your book's production is you.

(For the record, I convert the Markdown to rich text and do final formatting in Apple Pages for manuscripts that I'm submitting somewhere else. For novella-on-up length work, though, I'm one of those annoying Scrivener converts.)