My personal experience: I've tried using Leanpub and found issues with the way it handles mathematics. For example, the last time I checked (maybe around June) the TeX support in their Markdown was not developed enough to handle aligned equations, which is a big sticking point for me and I think for most mathematicians.
The standard process for academic writers is to typeset an entire book themselves in LaTeX regardless of the publisher (they tend not to publish-as-they-write, though that could conceivably change). Leanpub is unlikely to convince book authors in math by forcing them to convert to Markdown, especially for book writing when cross-chapter labels for theorems and exercises are common. If Leanpub wants to attract academic writers in math they need a sturdy tool that converts a LaTeX book to the Markdown flavor that Leanpub needs. But that's a crap-ton of work (especially considering third-party libraries like tikz) with an unclear contribution to Leanpub's bottom line.
Of course, the alternative is to post only a pdf format, but that kind of defeats the point of Leanpub which is that they generate multiple formats. A service like gumroad would be cheaper per transaction.