I agree that a zippered rear window would be great. However, the bulk of the zipper and extra fabric that covers the zippered section may make the top too bulky to fit into the top enclosure when lowered.
I do drive with the back section open, but I've been careful to use a bungee card to ensure that it stays up.
Two cautions: 1. if you do not use the bungee cord, be prepared that a hard bump could cause the back section to slam down, potentially screwing up the insert lockdown pin or holder not to mention scaring the crap out of you. (2) ensure that the top lid is locked back down or it could fly open at speed potentially bending the hinges.
While I have not had any damage, it has been due to blind luck rather than any technical talent on my part, but both incidents have happened to me.