An excellent example of an ebook which examines this is Kevin Klement's work on Bertrand Russell's _Introduction to Mathematical Philosophy_:
http://people.umass.edu/klement/russell-imp.html
Anyone considering this problem space would do well to examine his source files, as well as to compare the experience of reading the nicely formatted .pdfs and the ePub.
A similar comparison is possible between the version of Okakura Kakuzo's _The Book of Tea_ which I formatted using TeX (and which is in the TeX Showcase
http://www.tug.org/texshowcase/ ):
http://mysite.verizon.net/william_fr...ebookoftea.pdf
and the ePub version:
https://www.mobileread.com/forums/showthread.php?t=97542
William