Thanks for getting back to me and explaining the rationale behind the decision.
Are you 100% sure that adding a zoom feature, highlight feature, and a table of contents would interfere with the overall formatting of the respective pages? I have found that, while viewing PDFs for example, I can zoom in as much as I want and still remain on the same page.
Perhaps you could charge a little bit more upon adding those features, making it a win-win?
In any case, thank you for making the iBooks version in the first place, and for all your helpful tips.