It seems like you're getting confused between ebooks on the iBookstore and iBooks author books on the iBookstore.
The books that have the page turning animation are (for the sake of this conversation) ebooks - they do not have strict formatting and the iBooks application itself adds the page turning animation.
iBooks author does NOT create ebooks. It creates graphically rich text books (or picture books, or travel guides, or whatever else you want to make). These books have a structured layout, images, videos, 3d models, etc but they don't get the page turning animation. The page turning animation is only for ebooks at this point.
As far as I know there is no public facing system for making ebooks, only iBooks author books. To create an ebook you need to go through a publisher. They are 2 different categories of books that sit side by side in the iBookstore.