You're correct that we're more expensive per transaction than Gumroad, which is an excellent service. Now, for some books, the amount earned above the minimum price is more than enough to make up the difference: our price sliders work really well to earn extra money for authors. The Leanpub vs. Gumroad question is actually a really interesting one; there are other considerations on both sides. (Gumroad is what I recommend for authors who don't find Leanpub a good fit. I know that authors like Nathan Barry make a killing using their own sites for the marketing and Gumroad for the selling.)
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...
One thing that's immediate: the only math typesetting language serious math writers ever use is LaTeX, and I think in terms of "math mode" support it would be enough to fully support whatever subset of tex syntax is supported on sites frequented heavily by mathematicians, specifically mathoverflow.com (I believe it's MathJax with some extensions for special scripts and diagrams like [1]). It seems like the technology to get TeX->HTML is already there at mathoverflow, so I imagine it wouldn't be too hard to avoid reinventing the wheel.
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.
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...