good comments. the only thing I would add here is that the reason the dyno measures a loss in power (with exhaust) is a pretty interesting story. someone correct me if wrong, but if I remember the experiment correctly (Ted Jannety did this) the theory was that the decreased restriction caused better turbocharger spool up which resulted in slightly higher boost pressures for the same fueling level -- which means that the ECM would see higher than normal boost pressures and defuel. In other words, the designers knew what they were doing. Stock fueling and stock turbocharger need the restriction of the stock exhaust to produce the boost pressures that the ECM requires to produce the fuel associated with acheiving stock performance!
Note that this occurs only when the exhaust is changed. changing the intake system does not have the same affect on drive pressure as does changing the exhaust. In other words, I'm not aware of any decrease in performance when you change the intake w/o changing the exhaust. But then the question is why would you do that...
I agree totally with Robert, in terms of the reason why you would put an after market filter on the truck. the one that is on there was designed to support the truck in its stock power configuration.
there is one argument in favor of changing the factory air box on the stock truck, and it is not related to performance. Yes, the stock airbox is restrictive, but it DOES support stock performance. However, it sucks air right off of the right front tire and takes essentially none from the engine compartment. That means an after market open-element airbox such as the AFE may give an advantage in terms of total dirt entering the engine. my intial tests confirm that the AFE with PG-7 produced a reduction in silica levels and engine wear indicators (iron) via oil analysis. I'm not relying on this single data point as proof (single points do not make a trend), But I am suggesting that MY initial results suggest that you can get less dirt in the engine simply by not introducing as much to the filter. Engines don't care about filtration efficiency -- they care about the amount of dirt they actually see. For example, you can introduce 100 grams of dirt to a 99. 5% efficiency filter and get a half gram inside the engine. But you can also introduce 67 grams of dirt to a 99. 25% efficiency filter, and end up with the same amount of dirt dirt inside the engine.
now you can argue, certainly, that the DC engineers must have considered the stock filter to be sufficient. that has to be the case, but consider that their goals might be different from yours. they are interested in the cheapest production cost that will support their warranty statement. you might be interested in driving all wear indicators down to the minimum so that your engine will last as long as possible. They might not be willing to pay for the additional filtration cost, but you may.
Also do not forget that the stock airbox design, while it meets the stock performance requrements and warranty goals of the manufacturer, also requires frequent maintenance. you gotta change those things often! I was astonished at the amount of dirt after only 3,000 miles. Ultimately, if you have an engine failure that is the result of poor filtration AND you have the STOCK airbox, you're still not off the hook. That is, there is no safety in having the stock airbox on there unless you change the filter regularly. The first time DC sees dust in your intake tube because of an improperly installed or infrequently changed filter, you're in warranty trouble anyway. Thats what my dealer told me, anyway -- and THEY are still behind the times on the K&N story!