Someone has to benefit
Any educational model will always benefit one demographic more than another.
The school is designed to impart knowledge in the most efficient way. If girls are better at absorbing that knowledge, then so be it.
Schools are designed to provide students with knowledge in the most efficient way. Therefore, to say the school system is designed to benefit girls is a folly. It is designed to impart knowledge effectively. If girls are better at focusing/sitting still/receiving that knowledge, then so be it.
An inattentive, and lazy worker does not excel in the workplace. An inattentive and lazy student does not excel at school. There is no inherent design in the workplace that benefits the hardworking, just as there is no design in the school system to give girls a leg up. Girls are simply able to apply themselves and focus more, therefore, they progress faster. The school system is designed to impart knowledge in the most efficient way. The fact that girls are better at absorbing knowledge in that manner is not part of a wicked design to structurally alienate boys, it just means they are better learners.  Instead of worrying about how we can change the system to even the playing field, we should look at how we can change boys to make them more receptive to knowledge and focus better.
If the function of the school system is to impart knowledge in the most effective way, then surely it is committed to devising a way that benefits all students, not just the female students. If males and females learn differently and benefit from different learning styles, instead of choosing one which may favour one group, surely it is the school system's responsibility to pursue different teaching methods for different groups of students? By accepting that boys are struggling in the existing school system, but not taking steps to remedy the situation, the school system is not performing its basic function of providing a learning environment that is advantageous to everyone.
[P1] The school system is devised to impart knowledge in the most effective and efficient way. [P2] The school system is not responsible for creating a level playing field between the sexes. [P3] Therefore, it does not matter who benefits more from the school system.
[Rejecting P1] The school system's function is to impart knowledge in the most effective and efficient way for everyone. [Rejecting P2] If different sexes benefit from different teaching methods, it is the school system's responsibility to ensure those students access the teaching methods that benefit them.