There can be statistical differences on average, without requiring that every brain is unambiguously classifiable as "male" or "female" on a biological level based on that trait.
For example- if a drug works well for 80% of women and 15% of men, that implies that there are some men whose brains utilize the "female" pain pathway and some women who use the "male" pain pathway. It also suggests that that drug might be a good first line of treatment for female patients and a secondary or tertiary line of treatment for male patients. Trying to classify brains like this is like trying to classify sex based on height- on average it sort of works, but there's enough overlap between the heights of women and men that you can't actually do it reliably on an individual level.
So tl;dr I don't think that "clear biological differences between the male and female brains" is actually a reasonable conclusion that can be drawn from this research.