I think the stock sub is somewhere between 8-10". It's definitely larger than on 8" and a 10 seems to fit the rear opening nicely. A 12" would likely require some cutting. A simple MDF baffle in place of the plastic baffle used for the Bose sub should support a 10" and not hang down into the trunk too low. Some dampening of the rest of the necessary items on the rear deck will help with rattles. Don't put it all back together until you've thoroughly tested for rattles with all types of music.
Also note that an open-air/IB sub can easily over-exert itself and cause distortion and even damage. So if you have a girlfriend who gets excited when "her song" comes on and slams the volume up, be sure to keep your pimp hand strong.
If you use a low profile sub go as large as possible on the sub diameter as most tend to be excursion limited. The Alpines and JL Audios are some of the most capable in terms of excursion so they are less of a concern A 12" or even 15" should work fine firing through the stock opening and won't exhibit any bandpass behavior (no limiting of upper freqs from the mounting).