I found mention of a material called Shape Lock - a super-low-melt plastic, I think it's a high density polyethylene. It melts in hot water and you can mold it however you like. You could use that to mold a cap or plug to fill the gap at the top of your hatch.
I don't know where to find it; maybe a local craft shop like Michael's or Hobby Lobby? I know you can get it from a couple of Web suppliers.
Obviously the top of your car is going to be entirely too hot for this stuff to stand up to, but once you've molded the part you want, you could then cast plaster around the part, then make the part up from a more durable material using the plaster cast.
You'd think the manufacturers would maybe anticipate folks not wanting draggy roof racks on their cars, but nooo!
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