Vertical auto scaling is a good recipe for FAIL! This is the reader's fault. Its operating system was written by idiots. Why can't they just implement something like GoodReader on the iDevices, that lets you lock the zoom level you want and just let you scroll down, while maintaining that zoom level throughout the book?
This cropping that you speak of, should be done automatically if the document is too tall. Or at least have the option to zoom out a bit, while sacrificing some of the side real estate.