Actually these holes appear to be there to remove water that has entered the intake hose in the front of the car. Noticed that there was some residue in the bottom portion of the outer cover when I removed it.

Oh, btw, to remove the "bulges" you just have to pry back on the tabs located on the sides of the bulges. Be careful they are three years old and mine were a bit stiff. Easy to reinstall, just snap back in place!