I've seen one of the new Mini's with a Red Bull can on the back, with a fibreglass set up just like that.
I yanked the rear seats & seatbelt towers out of mine, and covered it up with a home-made vinyl/fabric tonneau cover.

There's a piece of wood screwed in to the factory holes (hidden, but in the bottom right of that pic) so the top has something to rest against when it's behind the seats.
I haven't even bothered with the rear window yet, but I had planned on half-assing a thin plastic window in there... Same idea, just velcro to hold it on.
Here's a pic that got me started on this:

I liked it so much, I'm just going to go ahead and have a guy work something up like that out of diamond plate. It's going to bolt right in, the pickup bed part will open like a trunk, and like you, I'm hoping to find a small rear window to fit in. I'm going to hinge it to lay back flat like a reverse jeep windshield so I can still be out in the open when it's nice, and have an easy place to stow the front half of the hard top.
I think the tiny rear window of my old '82 Toyota pickup would fit, but I haven't taken measurements.
-Al.