You're also correct that one of the main points of Leanpub is the one-click "make all the formats and sell them" approach. We do offer PDF upload for authors who find Leanpub's workflow preferable to more DIY sites like Gumroad.
Specifically, in terms of LaTeX support: we do support LaTeX math, but you're correct that there are some limitations. I'm not sure if the work we're doing on Markua (https://leanpub.com/markua) will help with this or not. I think that it will help with some of it (making equations into figures and referencing them from other places), but not others (probably the alignment isn't good enough). I'd really appreciate it if you could contact me with specifics if you want...
The other things are less math specific and more organizationally specific. If I were writing a serious academic math text, it would be full of theorems, corollaries, and exercises which I would refer to in later chapters by a label. For example you might put some simple but tedious computation as an exercise in an earlier chapter and then when using the result in a later proof you can say "The claim that BLAH is Exercise II.4.3." Leanpub appears to currently only have support for figure labels, but in math we often want labels for these other things too, which we can then reference across the entire book. In TeX, anything that is assigned a number can also be assigned a label.
Serious math texts also have a need for bibliographies at the end of each chapter and at the end of the book, and if there's anything a writer doesn't want to do it's alphabetize and manage labels for a hundred references. We have BibTeX for this, but Leanpub appears to have nothing. One could write a tool that translates bibtex output to markdown, but again it's a lot of work.
[1]: http://mathoverflow.net/questions/159655/commutative-diagram...
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.