Currently finishing my third (full-length academic) book in markdown. Wrote the second book in markdown too. Wrote the first book in MS word. Never going back.
Here's the thing. Word is a buggy bloated piece of shit application with an incomprehensible and ever-changing UI that requires 20 mouse clicks hunting through badly labeled menus to do anything. Latex is far too complicated for prose that doesn't have equations all in it, and is also unsupported by publishers outside of the sciences. Alternative word processors (OpenOffice, Pages, the desiccated shell of WordPerfect) are either buggy, ugly, unmaintained, lack critical features, or all of the above.
So I just write in markdown in emacs. Markdown mode in emacs works very well, I have hardly any customizations on top. One file per chapter. References in zotero, insert citations in better bibtex. Compile it all in pandoc.
When I want to revise I just concatenate the files and compile it to PDF and read my own work there. When I want to submit to a publisher I just compile it to word. I have a makefile that handles all of that for me. Then I make a few tiny tweaks in the garbage program and submit.
This is the best workflow I've ever found for academic writing, because pandoc-enhanced markdown and better bibtex enhanced zotero give you everything you really need for academic writing (like control over reference formats), and nothing you don't need (endless nightmarish word bloat). And you can just store it all in a GitHub repo.