Part of the reason for the airbox is the polution control system, when you swiis cheese the airbox, and/or remove the silencer you have effectively bypassed the thermactor part of the pollution controls. the purpose of the thermactor is to grab air from the heated manifold area which in turn makes your choke turn off faster (or in this case the computer program that simulates a conventional choke in the fuel injection system) and helps cut emissions by leaning out the mixture sooner. They also say it makes the vehicle more drivable during warmup but I never noticed much difference with or without ... in fact most cars with over a 8-10 years old don't have a working thermactor anymore and no one seems to even notice the difference
