I had a similar situtation in my install. you can see it here
http://www.mp3car.com/vbulletin/show-off-your-project/34240-stationrocket-wrx-done.html
I have a Diamond Audio 10" sub in a .5 ft3 sealed enclosure with about 5/8" between the back of the magnet and the floor of the enclosure. It sounds great.
I think you want to have a little bit of room back there so you don't cause acoustic problems but the back of the magnet isn't going to move so you don't have to worry about it crashing. I believe if you put some kind of fill in teh box you will minimise the potential problems caused bu the tight clearence. I got some from
www.partsexpress.com they have lots of good parts for this sort of thing but i don't think the actual subs they carry are all that great.
Also what sub are you using? There are lots of different subs out there with very different mounting depths. You may be able to get one that isn't so deep.
Are you taking out the spare tire? If yes it seems to me you should have pleanty of room for even a big sub. I left mine in there and managed to fit it in. My hard time was getting enough volume in the enclosure.