OK, this is just me. From my experience with building boxes and carpeting them. I have, and would, trim the carpet fibers themselves around the sub, not the complete carpet and backing. This can be done with scissors or a beard trimmer. I have done this for 2 reasons. 1, the carpet will prolly shrink a little over time, this will make the area around the subs look real stupid if bare wood is showing. 2, the rubber backing, by itself, will create a great seal between the sub and box. However you do it, if you use all the screw holes and all grab the MDF well (which is difficult) you will create I good seal. About grabbing the MDF, you can get (I can't remember the name of them) some blind nuts that hammer into the opposite side of the wood and the screws will screw into them. It makes for a nice, tight seal.
Robb