I was pointed today to another self-publishing house, Softcover, that also uses Markdown as the starting point for e-books on multiple platforms. Their approach is less turnkey than Leanpub, in that Softcover expects you to download the conversion software and run everything on your own machine. That has advantages and disadvantages—you have to redownload software to get bug fixes, but you have more access to the software to make your own workarounds or fixes. Softcover seems to be converting Markdown into PolyTeX, a subset of LaTeX, and you have the option of starting in PolyTeX directly (which seems like an easier conversion path from LaTeX than going all the way to Markdown). But you don’t have the option of just providing a PDF file, so far as I can tell.
The Softcover royalty scheme for their store (straight 90%-10% split with immediate payment) is slightly more generous than Leanpub’s (90%-50¢), but they don’t have the adjustable pricing of Leanpub, and setting up the store site seems more of a hassle on Softcover.
For now, I plan to stick with Leanpub, but I’ll look into Softcover as a possibility if I decide to try to produce MOBI and EPUB formats.