I am wondering about the same issue, as I am working on a pet project involving an audio eBook.
Specifically, I would like to customize the audio player control bar (not necessarily on iBooks --- for example Readium or Calibre ebook-viewer now support the audio element as per EPUB 3 specs). The EPUB 3 specs do not seem to provide much meat, nor the "official" samples do.
The support is --- surprise, surprise --- spotty. When I change chapter in ebook-viewer, the audio track that has started playing stops. On iBooks, on the other hand, this does not happen. So, if I need to listen to a different track (from, say, Chapter 2), I need to go back and stop the track associated with the previous chapter (say, Chapter 1).
Does anyone have good pointers to solve/document these issues? Thanks in advance.