sag2, what's your take on the seal around the edge of the stock box on the 4th gen? i haven't looked at my 2010 yet (just rolled 4000 miles), but I know my 01 had a terrible seal around the perimeter of the stock filter. I found dust trails on the clean side of the housing when the truck was bone stock. Some filter grease helped, but I was NOT impressed! The balance between flow, NVH and cost-of-manufacture seems to lean heavily towards the lower cost option.
I don't know how much the programmer developers (Mads, H&S, etc) are tweaking the MAF tables, but I know it can be VERY tedious and time consuming! My 09 Subaru WRX had to have a separate software load for each aftermarket air intake due to the different flow characteristics through and around the MAF sensor. Changing the intake tube's shape or size (and/or the filter, the sensor's location, almost anything) changes the actual mass of air entering the engine relative to the sample picked up by the sensor! Major PITA for the tuners...