Having done a lot of work with mobigen applied html files, I made a couple quick checks with kindlegen performing epub -> mobi conversion. On a simple book mobigen worked fine. On a more complicated book it said that it died trying to do TOC conversion. I tried Calibre2 ebook-convert epub -> mobi conversion on this more complicated book and ebook-convert worked fine. So, IMHO, another arrow in one's quiver, but "nothing special" re epub -> mobi conversion.
HOWEVER, kindlegen DOES come with a substantial OPF "Worked Example" namely the Sample directory, which appears to contain the source code to the entire Kindle User's Guide -- very handy to see how it *ought* to be done -- especially in regards how to set up an OPF file and CSS! The sample also comes with lots of cool graphics symbols relating to Kindle that might be useful if one was writing a review or guide to the Kindle -- but I guess one would have to check with Amazon about that.