FWIW, I agree most prose works great and think you're right that the technical book experience is where it's most clearly lacking (not being able to quickly flip to an appendix or back / forth 5 pages is a big annoyance of mine).
There are ways I think it works poorly for prose, though, too. The most obvious example to me is the George RR Martin Fire & Ice books. When I'm reading those, I very frequently want to flip from a section of the book to the maps of the world described in the book. I read a physical copy of the first two books but went to Kindle (both the 3rd generation Kindle and Android app) for the third and it's tedious to set a book mark, navigate to marks and notes, find the map, and then navigate back to the bookmark. Additionally, the map images in the ebook are of such low quality that they are nearly unreadable. Lastly, there's an appendix of the families represented in these books at the back (who's who). When reading the first two books, I often would consult that, too, but once I'd done that with the Kindle book, it made it really painful to switch back and forth between reading on my phone vs. my kindle, because the "sync" function is "sync to furthest page read" - which is at the end of the book, not my current place in the book.
All of the above gripes with that book would be plain to see for anyone who bothered trying to read the book on a kindle - and it should be obvious to the kindle team that "sync to furthest page read" breaks when a book has an appendix / index or something that readers are likely to consult.