Personally, I'm picky on the translation, so I'd place that far above the layout of the book. That doesn't mean I'd put up with sloppy organization of the text -- nor do I have to.
It might take some work and scripting, but now that Sony is pushing EPUB, you might want to pick up your prefered translation for the store and "improve" it. True, the version you buy will have to be freed from the DRM tyrany, but once that's done, EPUBs are easy to open and modify -- even by hand. It wouldn't be that hard to run a quick find and replace to insert at every chapter break a link back to the TOC (or better yet, your own set of TOCs) .
The next step in performance improvement would be Chapterizing the EPUB (one XHTML per chapter, as opposed to one per book). It would improve load time but would require much more than a simple global find/replace.
My advise, buy the translation you like, tear out the digital binding and put your own on.