OK..., second attempt at the margins patch for the Paperwhite, which hopefully fixes all of the previous issues. Download now available again at the original post.
Special thanks to DuckieTigger
for the extensive testing, and for the very helpful input!
While this version has been tested rather thoroughly (with .mobi/.azw3 books, and with .pdf files), I cannot guarantee that it will always work correctly under all circumstances. If you experience odd behavior, please report it here.
PS: Did I mention that Amazon did a great job in making their code look like complete rubbish? Thanks, Amazon, much appreciated. We really love to get fucked while attempting to make your devices more usable.