Here's something to consider: you've ditched MS Word, maybe you can ditch InDesign too? In my experience once content goes into an Adobe program, it's hard to get it out again in a clean way. It's pretty impressive what you can accomplish using CSS3 for print layout[1].
I work at an academic publisher, and I've spent much of the last year preaching the benefits of a similar workflow. Some of the editors are now editing manuscripts in Markdown files directly. Currently we're building a system where a single set of text files get fed into a program like a static website generator. This produces a web version, but also PDF, ePUB, etc. automatically. We're getting pretty close[2]. I think this is the future for many forms of publishing.
I think one of the big remaining pieces of the puzzle is creating a better Markdown editor, something suited for the needs of scholars & academics with support for things like footnotes, bibliographies, etc, while remaining a plain-text format.
[1] http://alistapart.com/article/building-books-with-css3 [2] http://egardner.github.io/posts/2015/building-books-with-mid...