- Is my understanding correct that the Kindle Fire and Nook HD do not support this kind of audio embedding for fixed layout?
* It's supported but you need to have a special agreement with Amazon or B&N to be able to upload enhanced ebooks. AFAIK, you need to be a big publishing house to be able to not go their self-publishing workflow and be able to sell it.
- How widely supported would a fixed layout EPUB3 file be with this audio feature? Would some Kobo platforms support it?
* AFAIK, only iBooks, Azardi, and Readium (Chrome Plugin) has support for this. I don't have personal experience if Kobo is able to support them but they supposed to be able to. You might want to check
BISG's EPUB3 Support Grid for a comprehensive list of tablets and epub3 features that are supported.
- If the book were only produced for iBooks, is there any advantage to creating an EPUB3 fixed layout file rather than an iBooks Author file?
* Building an epub3 has the advantage that if ever the other reader software especially ADE based ones will adopt epub3 standards your ebook will no longer need to be modified to be read on it.
- Are there any good examples of EPUB3 fixed layout out there that include this sort of functionality?
* I don't have specific samples since your looking a custom javascript for the audio controls but there are epub3 samples on AZARDI's site that has audio
here and javascript implementation that might give you an idea.