There's one BIG reason for a HTML Table of Contents - the Look Inside feature in the Amazon Store. Showing a prospective buyer the Contents in the 10% of the book that is shown can be very desirable.
On the general question, you need to embrace the difference between print and eBook layout. We are not defining the position of words and pictures on a page, we are pouring them into a container. The user is in charge of screen size, font size, maybe margins... There's no point in trying to be a control freak, it will just be over-ruled!
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