Yes, I can see how this would be a problem
I would say the best option is to open a "Wishlist" bug against calibre (
https://bugs.launchpad.net/calibre) and ask to see if it's possible for the QT window to scroll when the window is taller than the screen. Or if it already does that, then ask for the window to be opened at no taller than the screen height. And in the meantime, I'll avoid adding any options