Certainly I'm not terribly offended by the prospect of going with TeX instead of InDesign...I'm just more familiar with design software as it was part of my previous line of work.
With stuff with lots of linked endnotes like the ePub of Terry Pratchett's "Unseen Academicals", they're provided as distinct html files (27 of them). In the end, I just brought them in manually as footnotes in InDesign, which was a bit of extra work but not too bad. The bigger problems come from managing white space left by widow/orphan control, especially when combined with the bigger footnotes (page 1 of that book is a doozy).
I'm not too offended at doing things manually...but I worry that I'll spend more time redoing my books than reading them. It's a bit of idiocy anyway, since I'm not allowed to share my results unless I work solely with out-of-copyright stuff.
I should investigate Jellby's script more...anyone got any good samples of output? I'll probably search for them, but doesn't hurt to troll for recommendations.