The primary function of the school system is to educate. Therefore, when measuring the school system's fit-for-purpose it is imperative the scope is kept limited to academic outcomes.
To argue that the school system does not benefit girls more because of their mental health outcomes is like saying the transportation system benefits one demographic over another because they enjoy being on buses. The purpose of the transportation system is not to entertain or please, but to transport people from point A to point B, just as the purpose of the education system is to educate.
Any assessment of the school system's performance should be limited to academic and educational outputs and the demographics that over or underachieve. Happiness levels are not relevant to the discussion of whether the system is weighted towards female achievement.