There is no single ebook-friendly format. Different ebook readers are better/worse with different formats (mobi, epub, etc). Therefore, we probably need to be a little more explicit when talking about ebook formats.
One of the advantages of some ebook formats, such as epub, is that they can be more accessible for the blind and vision impaired than PDF or even HTML. There are at least two packages I'm aware of which will allow epub formatted books to also be read directly in Emacs.
My experience with Calibre is that the quality of the output you get depends on both the quality of input (e.g. poorly structured or poorly tagged PDFs will result in poor conversion) and on the settings of Calibre itself (of which there is quite a lot). I'm not sure how well Emacs documentation will convert. My experience with PDFs generated from Latex is not good as Latex is very weak with respect to accessibility and generating modern tagged PDF documents.