The Story HD does not have any settings for margins.
However with my UserStyle mod you can force additional CSS to be loaded. So you might be able to influence borders with that, since borders are just CSS properties also. However, depending on how the book itself specifies borders, you may not be able to override it with the userstyle.css
The problem is that borders can be specified either as border or margin or padding, for either html or body or even p tags. And these properties can even be negative. So it might not be easy to find a solution.
The more reliable method is using Calibre or Sigil to edit the books border definitions directly, but that works only with DRM free books.