I'm no engineer, but whenever an engine is upgraded for the purposes of making more power, etc, it will tend to move more volume. Since the demands of the engine are greater it makes the most sense to add more fuel. Air is added passively, of course.
If one were to adjust the mixture by removing air a correct ratio might be achievable, but it would not meet the flow demands (for lack of a better term) of the engine.
So basically, the best way to tune is to add something as opposed to removing something. Since air is added passively we will add fuel to keep up with the increased flow and make an ideal mixture.