Pete, It does change cam position. The proper position (straight edge across marks level with string) has to be set with the string at the 1/1 posts according to Mathews. I would set the brace height and axle to axle at the same time.
Then, repress and set it on your 2/2 pegs or whatever. When you are done with this, mark your cam location where the limbs cross the cam and write down the BH and AtoA. That way a quick look at the marks you placed on the cam will alert you to string or cable stretch and the need to retune to your new written specs without having to go back to 1/1..
Rick