Except in this case, variation in STEM performance is a cultural phenomenon, not a physical one. Imagine giving girls a place where they can concentrate on learning STEM topics without worry of being psychologically intimidated by the boys. Only once we've had a full generation of women who have taught that they can stand on their own will we be able to free ourselves from the inherent sexism in our society.
Racism and sexism aren't PC, so parents and teachers pay lib service to the new ethos. But subconsciously, it's still really bad. Peers, parents, and media still paint women and minorities as being inferior. Sure, we don't want thought police, but it's people's unrecognized and unadmitted beliefs that cause problems of racism and sexism to linger.
This girls-only STEM school is an attempt at fixing this. Maybe it'll open up its own new problems. But people are burying their heads in the sand about just how racist and sexist we are. It's closeted, so if festers and generates resentment among those who hate being forced to treat everyone equally, and this actually perpetuates the problem. We need to blow it out into the open and address it head-on.
Some of these problems would also be helped by making men take more equal roles in parenting too. Professional men with kids are seen as responsible. Professional women with kids are seen as a flight risk. That's got to change. And the law should come down REALLY hard on men who father children and then skip out. Some companies provide equal paternity leave, and that's a step in the right direction. If I were the CEO of a big company, I'd have the addition of an in-house daycare (free for employees) on my action list.