The PCM will adjust for proper air/fuel flow and timing anyway no matter what intake you have on, strock or aftermarket. The air going in quicker on a 3' pipe is not going to be a big deal. Then theres the MAF screen issue to contend with which will slow down the air flow anyway if you run a 3.5" pipe. I'm not going to pull the MAF screen or play with the PCM as the car is still under warranty. On a side note, my old Explorer had a 3.5" stock intake tube for a 4.0 ohv engine. The K&N FIPK kit had a filter with a 6" base that mated to the MAF sensor with no screen on it. The FIPK made hella power and great low end torque. The 3800 engine puts out more power and would surely be better off with a larger 3.5" intake.
If you notice the MAF is at the filter side, not the TB like on the 3800. Hell, diesel intake are larger yet. Coming from a truck background, bigger is better.