RTFA. The difference in pay was much greater than 1.5%. Men who became women took a 32% pay cut, while women who became men got a 1.5% pay raise. Assuming two trangsender people were earning the exact same amount beforehand, then the new women were earning only two-thirds the pay of the new men. That would explain the difference in pay between biological men and women.

I agree though that the study probably doesn't explain everything. I imagine transgender people look a little funny, and people who look funny won't get paid as much.