The point is that, regardless of whether the stereotype is true or not, this is a scientifically established psychological reaction that causes people to perform below their capacity, and it only affects those that are from a stereotyped group. This means that, in your example above, women will constantly be at a disadvantage compared to men in math performance.
Does it matter? If you were a member of such a group, I'd wager you would think it unfair, and doubly so since you are already trying to break a negative stereotype.