the stock air intake systrem is still in the car, but not actually being used, except for the last half of it....
The stock filter box has the bottom taken off, and the hoses all lead to the bottom of the box where it now intakes air from, it just blows cold air in the general direction of the intake area. The red filter on the top of the stock intake is actually just showing you how the filter looks that they made themselves. It normally sits in the filterbox.
this is all guessing btw