It seems there's a huge opening in the market to make an end-to-end publishing solution. We're all taking this scrappy approach* to making our books work cross-device. It's something I'd gladly pay for.
I just shot you an invite to the PenFM beta, because you hit it on the head. www.pen.fm is taking on that end-to-end publishing challenge, and then some. Having worked in epublishing for a few years now, I think I've finally come up with a way to automate the hell out of epublishing--and the results show up. At any point in writing in PenFM, you can click download and get your work formatted perfectly in epub, mobi, or pdf. Formatting improvements are coming rapidly, and mostly present already for mobi.
The biggest problem I've recognized with epublishing is that you have to get the formatting down perfectly, and usually that requires a lot of work by hand making sure your input HTML file is exactly as it should be. When you control how content is inputted to a platform, it's much easier to automate perfect-formatted rendering of that input HTML file, including TOC by inference.
My service, http://bookspry.com, does something like that. It's still in semi-beta (which means I'm taking paying customers, but the "do-it-yourself" plan is still very much the "I'm-doing-it-for-you" plan, since you'd be shocked at the bizarre formatting options people put into their Word document that have to be cleaned).
The biggest problem I've recognized with epublishing is that you have to get the formatting down perfectly, and usually that requires a lot of work by hand making sure your input HTML file is exactly as it should be. When you control how content is inputted to a platform, it's much easier to automate perfect-formatted rendering of that input HTML file, including TOC by inference.