@snowstone: Yes, buying from Amazon requires importing to calibre (with the assistance of everyone's favorite Apprentice) and converting to ePub. I just convert directly to KePub since the destination is my Kobo device and no other reader, and I always keep the original .mobi/.azw/.azw3 file.
@JSWolf: I wasn't always so knowledgeable about what's Kobo's problem and what's the publisher's problem
Although Kobo especially has no excuse for broken books like that since they pre-process them to add the KePub bits. I can detect when files aren't in the TOC or when a file in the TOC is missing (in fact it was more work to ignore that) so I can't imagine Kobo can't do it. Amazon also likely has no excuse, but I'm not familiar with what preprocessing/detection is done or possible with their formats and I've never bought a bad book from Amazon. Although I did get a book gift which only made a .HTMLZ file available to me (even syncing directly to a Kindle).