[Leanpub co-founder here.]

We use Markdown for authoring (one of two dialects: either Leanpub Flavoured Markdown or Markua).

We automatically produce PDF, EPUB, MOBI (what you were saying, essentially), but we also produce InDesign export. If you have a designer, give him/her the InDesign files. You can then produce exactly what you want as a finished product for print, with as much design as you want. But while the book is in-progress, nothing beats being able to click a button to publish.

...and if you don't want to do the InDesign work, you can just click a button and get a print-ready PDF file automatically produced by Leanpub.