For what it's worth, it used to be pretty standard to put the ToC at the back of the book when making epub and mobi files.

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.