It reduces the intake diameter/size to the air filter under 4K rpm. Which, in turn, increases the velocity of the intake airflow (including to the MAF sensor) in the 0-4k rpm range. Removing the entire assembly will only give you minor gain @ the top end 4-8.2K rpm (and then only with a K&N or similar high flow filter) and can possibly make the 0-4K rpm range a lil sluggish due to the reduction in sensed airflow.
It also keeps the intake noise down a bit under 4k.
While only a guess/theory on my part. I suspect that: given the fussyness of the MAF sensor, the unique housing for it, and the troubles with cold air intakes; there may be a small problem with the MAF sensing changes below a certain velocity and that Toyota added the butterfly to increase the velocity of the air to make the MAF readings more accurate under 4K rpm. That and the intake noise... there are no resonators in the stock intake, similar to other factory intakes (including Toyota), to reduce intake "drone".