There are certainly arguments about the actual extent of the pay-gap. But when you include all factors and make conservative estimates, you still end up with a statistically significant pay-gap. There is debate about the size, but not the existence. 

However, that doesn't really factor into this article. The lawyers were clearly able to prove the existence of a large wage-gap in how this woman was paid. Larger trends are irrelevant, and allowing the city to make adjustments for gaps that they do find is common sense.