Well, no, your publisher will NOT tell you what word processor to use. At least, in almost 40 years of writing books for publishers like McGraw-Hill, I've never had one do that. Content is the important thing. All else is format, and they handle that routinely.

I started writing books (novels and textbooks) when all I had was a typewriter. Since then using XyWrite and now Word, I've written fifty or so books. Given that experience, I would say that while the things you list would sometimes be nice to have, none are essential. Take notes as necessary and maintain tiered backups (today, yesterday, last week, last month), and you should be fine. At the moment I'm working on a book on 3D printing (Futurist article available below). Initially, I gave each chapter its own file. As the chapters approached final form, I merged all into a single file, which is now (thanks to illos) over 16Meg. Tom Easton http://www.sff.net/people/teaston/