If the question is "Do I have to convince a paying client that this is the best eBook structure?" the answer is no. I know, I am lucky. I am the author and self-publisher but also the only responsible of my results.
Instead of spending a precious time learning how to design eBooks, I could have been a "paying client" myself. My perception as a client, is that eBooks are changing the way books are produced and consummed. It is not only a physical change, it is a BIG change in readers purchasing and reading habits. Consequently, as an author, I have to adapt my books to this change, I have to change myself (I know, nobody like changes). So, I am extremely sensitive and open to what profesional publishers recommend me (This is actually what I am doing now). If their recommendations are oriented to help me sell more books, and they convince me of that ... "please, go ahead".
That said I understand your frustration, as a commercial publisher, to have to justify a change that is controlled by Amazon, not you. My life is so comfortable as an indie author ...