well, if the speaker holes are the only way for the bass to travel through... then i wouldnt do that neccesarily. maybe face the ports up, or the sub up, or both. but i wouldnt have the ports go up through the holes. just my .02
i believe they do that fopr the same reason a sub is louder when facing a corner. it bounces off and around more. i think the pports a few inches away would be fine, just make sure the rear deck is sturdy. what you should really do is try it both ways and see what you like best. unless, that is, your box cant be mounted both ways do to room limitations. but you should be able to.