In my mind since the filter media is downstream causing positive back pressure the small restriction that the fan was designed for should play no role on the cfm efficiency of the systemDoes the cover on the fan affect air flow? Pulling in thru the vent slots as opposed to full fan face open to the area.
Just curious, I left the cover off mine (because it was a bad fit when mounting against 2 sides) but if it directs the air out of the unit better I might have to look at cutting mine down to size and installing it.