This is the underpinning of an actual discrimination lawsuit, which has been taken against MIT, Cornell, Harvard and a few others. It makes exactly your argument: because fewer women apply, and the schools are keeping the gender balance neutral, de facto it means that less qualified women are getting places over more qualified men.
In real life there is no actual evidence that the women who are getting into MIT or Cornell or whereever are actually less qualified or less ‘excellent’ than the men who are getting in. All any of us have are the individual cases we see, and as others here on CC have pointed out, "the plural of anecdote is not data’.
And I for one am tired of the ‘oh it’s an advantage to be a woman in STEM / applying to MIT / etc.’ as if all of the other obstacles - large and obvious / small and subtle- involved in getting to the point of application (nevermind admiission) don’t exist. K-12 is still effectively a weed-out class for women in STEM (yes, lots of progress is being made- but there is still a seriously long way to go- just b/c you see a lot of headlines and hashtags doesn’t mean it’s all better now), so it stands to reason that the ones who make it through are likely to be stronger than average candidates.