Hi Bill,
Had the same problem and for this reason I purchased a cover from Bruce.
http://www.aircraftcovers.com/
He has an extended option that covers the avionics covers.
Doesn't help your inflight concerns. I did have clear 3M tape, similar to paint chip guard over the seam and fasteners until my cover showed up. Since I'm pressurized I don't have the inflight concern.
Dan
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Colorado medical marijuana