Its simple really, the internet books publishers are dealing with ePubs and although iBooks Author creates "books", its better to think that its an "app". While all the different publishers modify the basic ePub as we think about it, to suit their own storage, distribution by download etc,. most seem to understand that and accept it.
Apple does the same thing really with iBooks Author.. which was designed solely with one purpose.. allow anybody with the equipment and time, to make books for publication only to the iBooks store and viewable only on iPads - and now Mac computers with Mavericks installed.
So although you dont like the idea... distribution by "cloud" ie Dropbox etc,. allows anybody to send a ibook file direct to an iPad where it can be opened in the iBooks app.
Basically if its your choice to use Apple free software to make a book... then you have to accept the ifs and hows available to you and plan around it, What other book suppliers do with their products... they cannot do with ibooks.