We did it at Leanpub, and I'm pretty sure we were just following what the Prags and (if I remember correctly) O'Reilly were doing.
The reason was that opening an epub and flipping through a long ToC before you get to the book is really annoying. There is a way to set the "starting page" in epubs, but many ebook readers ignored this at the time and just opened at the title-page, so putting the ToC at the end was just a better reader experience.
Now that most e-readers use the start-page setting properly, ToCs are mostly at the beginning of ebooks.
(Trust me on this: I've known him in meatspace for about 15 years and he's simply not technically-minded enough to be trying to game the system: he's a novelist, not a programmer.)
Given that Kindle Unlimited is available in France (according to http://ebookfriendly.com/kindle-unlimited-ebook-subscription...), I wonder what they do...