I am not sure which exactly schools are discussed here. but I think a number of such schools have kids from less observant families to begin with – who view a Jewish school as a good prep school with Jewish kids, with varying attitudes towards religion. Of course, we hope that these kids will be affected by the school to the better, but it may not be the case. So, we need to count outcome separately based on their family history. This is similar to some teacher/school evaluation metrics that look at the improvement by the school comparing with what kids were before, rather than looking at current grades.
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