Hmmm, I don't know much about fluid dynamics, but could the smaller inlet maybe cause the droning, verses the 3" inlet?
What I did on the BRZ was add additional sound mating. Its an extra step, yes, but it also cut down road noise dramatically. I used this product:
http://www.protectowrap.com/flashing.../bt20xl-butyl/
It works great because its only 4" wide and is very flexible. This company makes an audio sound mat, which is made form the same material in hte product I posted. Only difference is that it is twice as thick and cost 2 to 4 times more depending where you go to buy it. I wish I had the photos of my BRZ to show you.
Some strips on the trunk floor and along the trans / drive shaft tunnel would make a big difference