Markdown. Its only in tech-spaces that its preferred, but it should be used everywhere. You can even write full books and academic papers in markdown (maybe with only a few extensions like latex / mathjax).
Instead, in a lot of fields, people are passing around variants of microsoft word documents with weird formatting and no standardization around headings, quotes, and comments.
Man, I've written three novels plus assorted shorter form stories in markdown.
There's a learning curve, but once you get going, it's so fluid. The problem is that when it comes time to format for release, you have to convert to something else, and not every word processor can handle markdown. It's extra work, but worth it, imo.
Pandoc + [your markdown editor of choice] is magic. Some editors even come with Pandoc as a dependency so you can export to more or less anything from the GUI. I think GhostWriter and Zettlr at least (I honestly can't be sure, I've changed editors so often and now I just have some Pandoc conversion scripts in my file manager menu).
Publishers are pissy about such things. Even self publishing (which is what I do now), the various outlets still have limits to what they will use. Amazon accepts something like three file formats, including their own, and pdf isn't on the list.
I could just do pdf for directly giving them away to people, but even then, epub is usually a better pick in terms of readability since that's the standard for actual books since ereaders tend to display it better than pdfs. Most people reading books via files would be using something that can give a better experience with epub vs pdf.
Markdown is awesome, I agree! I did not realize you could extend markdown with anything other than html. The html extension is quite nice to do anything that markdown doesn't support natively, but I wish there was an easier way to extend markdown. Maybe the ones you listed are what I need.
My main wishlist for markdown, is a better live collaborative markdown editor. Hedgedoc works, but it's showing it's age, and they don't seem to be getting close to releasing v2.
Etherpad also has a markdown extension, but it doesn't import / export that well.
Depends on the type of book. Since you need HTML for all non default styles. Therefore, it raises the bar... you need a bit of web dev knowledge which removes the biggest benefit of markdown: simplicity / ease of use.
ReST (restructured text) is a good middle ground. I just wish it had more support outside of the python community. It could use some new/better tooling than Sphinx