If we were talking about an epub reader, I would suggest using the @page CSS rule. With that, you could set the bottom margin if the page to whatever was needed to prevent anything from being displayed in the bad section of the screen. Something like the following would probably work:
Code:
@page {
margin-bottom: 3cm
}
With appropriate testing of how much to set the bottom margin. And I have no idea whether cm works as a margin here.
I don't use a Kindle, so I don't know what would happen if you converted an epub that has the above to a Kindle suitable format.