I'm going through the same decision, except that my truck is bone stock.
From the first dyno plot, it seems that the stock kegger intake has the best torque and hp until about 4000 rpm when the Airgap takes over. In the second dyno plot, (after an SCT retune) the Aigap is slightly better than stock below 4000 rpm, and much better over 4000 rpm.
My truck (1998 5.9) redlines at 5000 and I rarely go above 4000 (esp. with $4.50 gas), so I have decided to just buy the aluminum plenum plate and stay with the stock tune. It is too expensive to go the other route ($600 for the intake and $500 for the SCT).
If you have modified the engine significantly: exhaust, heads, valvetrain, supercharger, etc. and want to enjoy the high rpm performance, then you would benefit from the other route.
I believe that the aftermarket intakes are all sealed at the bottom, so they have no plenum plate or gasket to worry about.
The stock intake was designed specifically for fuel injection: long runners and large plenum space. The other intakes are really designed for carbureters, then later adapted to fuel injection. Intakes for carbureters have a design to promote atomization of the fuel/air mixture. Fuel injected intakes only have to deal with pure air. The fuel is injected at the very end of the runners. This is just my understanding after doing a bit of reading on the subject. If you look at the intakes on modern engines, such as the newer Corvette, it has long runners like the stock kegger.
Just my 2 cents.