It's been done before, I remember christofoo's Civic ecomodder.com: Project: ECOfamily Civic and its Aero Hitch Box / Boat Tail
There have been others.
I like ecomodder.com: MetroMPG's Honda Insight boat tail extension (cardboard) tuft video; ABA test +9.7%. It doesn't have a gap a-tall.
Possible solutions: a hinged flap for access to the lift-gate latch. Or the whole box slides back. The downside of filling it with cargo is the vehicle will oversteer like a VW Beetle. 
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