That's a major reason why there's a disparity. They are looking at the whole workforce. Men and women in the exact same job earn equal pay. If anything, the women will tend to earn more, so they won't have any excuse to sue for pay discrimination.
But if you look at the jobs that involve dangerous or uncomfortable working conditions, that involve being on the road a lot, that involve lots of mandatory overtime -- they are mostly filled by men. These jobs naturally pay more than safe comfortable jobs. Otherwise who would be interested in them?
Some of the most dangerous jobs (roofer, lumberjack, commercial fisherman) are nearly all male, and don’t pay particularly well.