Jimmy,
I have been looking at the ATI Commander in 9mm, and in my research, I watched Hickok45's review of the 45. He also encountered that the ATI Commander in 45 shot low, and he filed down the front sight. Unfortunately, he lowered the front sight as much as he dared, but it didn't fix the problem entirely.
From what I could see, the front sight is staked on, not a dovetail. When my 9mm Commander comes in, IFF it shoots lower than I am comfortable with, I am contemplating having an adjustable Novak rear and a Novak front, so it will be close to identical to my Ruger Commander in 45.