I'm probably going to be proved wrong in my statement: I do not like carrying a spare, or much of anything, on my roof for fear of raising my center of gravity to much. I now run 33x12.50 BFG MT's on 15x8 steel rims, I don't know what they weigh, but they aren'y light, and there's no way I am a)going to put that much weight up that high, and b) no way I am physiclly going to chuck a tire like that up and onto a roof rack.
I used to have my 31's on stock steel rims, and I used to have the spare up on the roof on my old roof rack. Maybe I'm nuts, but I swear I could feel the diffrence both on the trail, and on pavement, with it tossed up there. Granted, back in the day I also ran no swaybars half the time.
A week ago I went on a simple wheeling adventure, w/o my spare. Tore a 3" gash in one of my BFG's, plugged it with a shop rag, sheetmetal screws and 1 can of that fix-a-flat. Kept topping it off with air from my OBA, and limped home for 10 miles on logging roads, and 20 on pavement. Travel with no spare, never again.
So in short, my opinion is to either make it fit on the OEM holder thingy inside (which you are trying to get away from), or put it on a rear swing out type setup. On the latter, I don't see a 31" being a problem. Hanging up depends on how the tires mounted, I've seen a few designs, and frankly some of them really were lame. Now if you don't wheel, or don't wheel alot (with off-camber situations, they are what scare me with a spare on top), I suppose you can make an arguement for on the roof. But personally, I don't like it up there.
It's a bit long, but there's my opinion.
Chris