I don't think it was designed in any particularly deep sense. The needs of men were slightly more taken into account, but do you really think all the contradictions like (1) lauding collaboration and open sharing of knowledge while (2) engaging in cut-throat competition to publish in paywalled journals is really designed to benefit men? Or an ethos that is (1) nominally highly socially liberal and caring but (2) expects you to work 60-80 hours a week and get lucky just to stay competitive and not disparaged? Or (1) training and evaluating people based on their scientific research accomplishments in order to (2) become managers and writers with only a modest and ever-decreasing amount of time to pay attention to science?

It seems mostly a consequence of the social and market dynamics with nobody minding the store. Fixing every intentional or mass-sentiment-based male preference would still leave the system nearly as badly flawed, it seems to me.