I've never noticed a lot of difference in the noise, though I do have to have a very hingh nocking point for three under, especially with a heavy tip weight (anything over about 200grains). My nock point is about 7/8" above square - as is my wife's bow, and she also shoots 3 under with a heavy broadhead.
Too low a nocking point will slam the arrow into the shelf, making noise and causing the arrow to rebound, and appear in the target as a high nock point. I stand back 30 - 40 yards from the target and adjust the nock point until I get good, clean, arrow flight.