willie, I doubt there would be any problem with it.
I'll bet the areas are open because your boat came standard with a motorbox cover and two rear seats back there. So those gaps were just the normal under the gunnel area ahead of those seats.
You could always cut out some wood or something to shape, temporarily install it, and then take the boat out on a HOT day and see if it caused any vapor lock or loss of breathing ability for the motor.
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I'm just happy to be here!