They did not "flip cause and effect on its head" - There is strong evidence for positive causal returns to education: https://www.sciencedirect.com/science/article/pii/S073805932...
So, an individual student will be expected to have higher earnings with more schooling. But as a matter of public policy that involves taxpayer funding of higher education, I cannot accurately base those decisions on a methodology that assumes a cost of zero ("no direct schooling costs").
Your source also identifies that higher marginal returns are found in lower-income, lower-educated countries, which makes sense. How much marginal return (for the taxpayer dollar) can we expect in a high-income country with a service-based economy and a third of the population already having a bachelor's degree?
The study measures benefit of education. If you wish to determine whether cost>benefit, join it with research on the cost of education.