I think the flap was intended to just drape down into the open space behind the metal panel. My factory boot only pops out from that location when there is a stiff craoss wind. So at least 95% of the time there are no issues.
I agree. I have always tucked it in that way. This is the factory original boot. Only once, when I first owned the car, did I have a problem with the wind blowing the boot out. Then I discovered that I was supposed to tuck the folded top in before lowering it all the way.