I believe that the box part of the intake is vacuum formed, so there shouldn't be any variances in size. I have no idea why mine sits so far back. I did remove my battery tray and a bunch of other parts in that area to install my chirp alarm, so maybe I put something back in differently (so many clips/tabs on this car).
I ran mine yesterday with the top cover removed out of curiosity, and it's still not loud at all. I think it must have to do with the piping being plastic. That, and I'm not sure how close the under side of the hood rests to the top of the intake. I may try to find a place to shove a GoPro under the hood to see. I didn't really want noise in the first place, so I'm not at all disappointed.