Well if you actually did make the box' internal volume a bit large that might compensate somewhat for the too large reflex port. The changes will probably alter the systems characteristics a bit, but I doubt if it will have much negative influence on the sound quality, if any at all.Mind you, reflex boxes CAN be very sensitive to alterations, but given the fact we're talking about a big box with a pair of relatively small, stiff suspensioned drivers there is more margin for mistakes... To my experience at least. And as you mention yourself, having the ports on the backside makes it easier to experiment without messing up the look of the box.
Just my two cents. :)