I think you could put a flexible plastic or rubber 'skirt' around the edge of the hole, that would just bend out of the way for the bike frames. seal it to the trunk lid with some silicone. I bet it would minimize leakage.
That was a huge score, getting a trunk lid that bolts on.
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2007 Dodge Ram 3500 SRW 4x4 with 6MT
2003 TDI Beetle
2002 TDI Beetle
currently parked - 1996 Dodge 2500 Cummins Turbodiesel
Custom cab, auto, 3.55 gears
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