There is an AFE now with an integrated torque tube. It is called Stage 2. Depending where you get it, it is about the same price as getting the Stage 1 and the torque tube. The Stage 2 has a cover for the box whereas the Stage 1 looks like it seals to the hood.
The Scotty III is a bit cheaper but uses the stock intake tubing.
Basically the concept is the same in both of them. The air into the box is from the same place - the stock inlet plus open to the front which is non-stock. Scotty calls theirs a Ram Air but I doubt it gets pressurized much. Piers sells Scotty III with AFE filters if you want or a foam filter.
I'm getting and AFE Stage 2 because I think it looks better, I don't need a separate torque tube, and servicing and inspecting the filter should be easier than on the Scotty. genosgarage.com has a good price on the AFE.