Yeah, you're probably going to have to settle with the fact that you're going to have to have a speaker box sitting in your trunk. If you get a smaller 8 or 10 inch sub, you could get a "small sealed box" that won't take up much space, and then just mount the amp onto the box. That really is probably the only way to go to conserve space.
It might be too much trouble to try to mount a speaker in the spare wheel/tire