I would say it might help, but that piece of rubber is not flush to the exterior hole, so in stock form i would guess it flows just fine with it on with the stock holes. The stock holes are just ridiculously small, enlarging them is the key to this mod. If you saw the 24 hour car early in this thread, they completely cut out that whole section of fender and the fender cover. I would really doubt removing the rubber by itself would increase the efficiency of that vent at all. In the stock form more of the air actually exits through the gap in the door and fender, not the vent. This is because of the great amount of restriction by the little fender holes. (recently i enlarged the holes even more then what is posted in this thread. Every bit helps.)
-To really test your theory, get your car hot enough to kick the radiator fans on and have one rubber piece in and one out, then feel the air flow.(the best way would be with mounted temp gauges while driving, but not a common item in the garage). When my fans kick on there is a huge amount of air exiting the fender vents.