The desktop reader lets you adjust margins. What if you adjust them there and then export the book to the cybook? Will that do anything?
I think the software needs to let us adjust our own margins, like it lets us adjust font sizes. To each his own. I don't think margins should be pre-set while making a book, unless the book is just for you. These books have to display well on many different devices and have to please many different readers.
Feedbooks creates pdf files to your own settings, including the size of the document, margins, font size, etc. You can play with the settings to fit your reader the way you like it. I've just made one 50mm square and sure enough, that's the size. Of course feedbooks is only for public domain or creative common documents.
http://www.feedbooks.com/