As with most cases, anything is possible with enough money. The question is, is it worth it? I was considering going the same route and just cramming two pipes right next to each other, following the stock path and just splitting the pipe from the driver's side header off to the driver's side after the spare... or just running them straight out back, side to side. Where it starts to get tricky is the actual physics of it... now, I'm just going to pull some numbers out of my ass, but assuming you were putting in two 2.5" pipes, that's roughly a 5" cross section per pipe, times two... so you're getting about a 10" cross section... put in one single 3" pipe, and you've got roughly a 7" cross section... now, I know that's a lot less, but you need a minimum of a 3" by 3" space to fit a single pipe in, whereas you'd need a minimum 5" by 2.5" space to fit dual pipes... the extra two inches could make a difference.
Also... you'd be able to flow more volume with dual pipes, but would you really need the extra flow? I'm not sure how many people put 3" exhaust piping on a 4.0, and the extra 3" cross section you'd get from a dual exhaust kind of seems like overkill, not to mention the difficulty in running dual pipes to the rear of the car. Any potential gains could be lost through all the bends in the pipes.
Then again, I'm no physics major, and I've only completed high school physics, so perhaps someone else has the knowledge to back me up or prove me wrong... personally I think that the cost (of parts and labour) outweighs any potential gains... you could probably get a better improvement with some other mods.
HTH,
Fil