Oh well, I was hoping I'd missed something. I'll just keep doing what I'm doing now -- write it in Evernote and then copy/paste when I get back to a computer.
I've found Simplenote on the iPad and Notational Velocity or nvALT on a Mac to be a really lightweight and quick workflow. Plus, there's the added benefit of it all being plain text, whereas Evernote always seems to make guesses about unwanted formatting for me.
Here's an iPad app that does Markdown + LaTeX: http://eqeditor.com/writer/ and then outputs HTML, ePub, etc. Not sure if it's exactly what you need but there you go.
Is the HTML generation with backlinks from an external lib or custom built for softcover? I'm working on a CMS and this would be fantastic to use as a module for writing articles.
http://softcover.io/
I use Softcover to write and maintain both the code-heavy Ruby on Rails Tutorial (http://railstutorial.org/book) and the math-heavy Tau Manifesto (http://tauday.com/tau-manifesto). (Disclosure: I'm also the principal author of Softcover.)