I don't think so anymore. I wrote a book for O'Reilly in 2016 (http://flyingsquirrelbook.com/) and it was done in ASCIIDoc, which is a variant of Markdown (or perhaps vice-versa) with some custom extensions and structures.
> which is a variant of Markdown (or perhaps vice-versa)
Neither, AsciiDoc has similar design goals to Markdown but it's a completely separate markup language. I like to explain AsciiDoc as a markup language that sits somewhere between Markdown and LaTeX, it handles far more things than Markdown (and is therefore more complex) but isn't nearly as complex as LaTeX (but also doesn't handle nearly as many things).
Behind the scenes, you're actually getting well-formed HTML5—specifically, HTMLBook, our new open standard for writing books (or book-like projects) in HTML.
If you prefer writing in one of the lightweight markup languages popular today, then we've got you covered with the Code Editor. In this text markup mode, you can use Markdown, DocBook XML, or AsciiDoc, a language similar to Markdown but more robust for presenting complex information.
I built the Atlas system that O'Reilly uses to produce books, along with a Markdown and Asciidoc converter to HTMLBook. So even though you write in Asciidoc or Markdown, it gets converted to HTMLBook since that's what the entire toolchain understands. But those formats are great for the authors wanting to write in a plain-text alternative.