I had an MX5 about a decade ago and the handbook said to unzip the (plastic) rear window and lay it flat before opening the roof. That was to stop it creasing and scratching (from dirt trapped where the window would fold back on itself if you didn't unzip it first). It took only a few seconds to reach back and unzip the window before throwing the roof back at traffic lights, but it was a bit more fiddly trying to zip it back up from the driver's seat without snagging the zip on the fabric.
So, if you put a zip in glass rear window into the roof it seems to me that so long as you've got something soft for the window to drop onto you can just unzip it before lowering the roof, just as FredH says above.
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