I think that Kindle is really the only one that does the seamless sync you're looking for, especially with audiobooks. Kobo offers audiobooks as well, but I don't think they offer any kind of whispersync-like functionality.
About whispersync: if you go onto the page to buy the kindle book and whispersync is available, you should be able to buy both formats at the same time and get a discount on the audiobook.
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