Correct me if I'm wrong, I am, however speaking from personal experience. The stock airbox will be more beneficial to a DD mustang (or any car for that matter) as it provides pressure whereas the ol tube on stick has none/little/creates a vaccum effect - depending on the design when driving under partial throttle conditions. A well designed stock box should create an environment for the air inside the box to be immediately available with gusto in relation to the TB.
Anywho, that's how I understand it. Stock airbox always gave me more torque in the lower rpm range when driving partial throttle.