Mytake:
Your question was why do the schools teach the way they do. My answer is that this (teaching Gemorah without any emunah, secular studies, etc.) is the best way to produce a possible Gadol, and if some or even many fall by the wayside, that is (in their eyes) a worthwhile sacrifice. The girl point was that even though girls schools don’t need to create gedolim, they follow the “meforshim” tract of the boys, just in Navi & not Gemorah.
I like ItcheSrulik’s response. I read it as “its much easier to teach Gemorah than it is to teach Yisodos”.