Hi, LaTeX copyeditor and typesetter here. The bane of my existence are authors who know just enough LaTeX to be dangerous. First, almost all of their formatting work is the first thing to be thrown out. Second, authors are strongly incentivized to learn the bare minimum of LaTeX to do what they need, and to copy-paste furiously whatever stuff they find on the net. You have to remember that (La)TeX is both a markup and a programming language. Can you imagine spending your time reading code written by a copy-paste monkey? I can, and don't wish you the pleasure.

LaTeX is fine for putting out pdfs. It's not a sufficient skillset for putting out an ebook in any other format. It is still a pain to put out a math-heavy book in a wide range of formats. I would say that Softcover (Michael Hartl's effort) is making that a lot easier, but I can't use the full range of LaTeX there (for reasons discussed elsewhere in this thread) and I still need to visually check every format to make sure that formulas are typesetting appropriately, because I'm trying to push the boundaries of current implementation -- and that's just in writing about probability and linear algebra.

In addition, if you really want to put out a quality product you have to be aware of how each e-reader renders the stuff you send them. Different e-readers process the same file differently and not all support the promised features of epub 3.0. It's best to know up front what each supports in terms of images and scaling, and then write with that in mind. Again, far beyond latex.

Division of labour tends to increase efficiency. Do you really want an author spending hours reading LaTeX tutorials, or do you want them to get on with their personal specialty and let a typesetting specialist do the typesetting? Either way the ultimate cost is going to be similar.