The "enclosure within an enclosure" refers to the bandpass effect that is created when you place any speaker box inside another box even if it is open on the front. The cabinet volume, shape, and even material it is made from will effect the sound being produced by the subwoofer(not to mention the possibility of induced noise created by rattles or hums from the cabinet itself). Sometimes this will make the sub louder at certain frequencies, sometimes it will make the sub sound muddy or flat. Next time you do this, run an RTA on the room with the sub in the cabinet and then pull the sub out of the cabinet and RTA it again. You shouldn't even need the RTA to hear the difference. I have seen installs where the cabinet so adversely effected the subwoofer that the sub sounded better with a solid door in front of it with the door closed. In the average install, this approach will work becuse the average customer doesn't know thatit can sound better, but in a high-end, custom theatre, this is another compromise that shouldn't be made before all other options have been explored.
Note however that if you are planning on the cabinet as the sub location from the design stage and you are having the cabinet built to house the sub, you can take steps to insure that the sound produced will be what you want.