Yes and no, with some explanation. I do not like to run the actual port from the box into the rear deck in most applications. As alphabets said, i think quality suffers. You're losing a certain level of acoustic coupling between the port and woofers, unless the rear seat is removed and the woofers are exposed into the cabin. The amount is slight, but in some applications it will still hurt.
In a situation where the trunk is tightly sealed from the car I like to do a normal ported box facing rear, and remove a portion of the rear deck to allow bass into the car.
In most cars where the only thing separating the cabin from the trunk is a foam seat and some carpet trim panels there's nothing to be gained by doing anything.