It seem there are two issues at hand:
1) Women who are in tech get paid less then men.
2) There are less women in tech to begin with.
They are related, in multiple ways perhaps and it's possible tease some links and accompanying explanations:
a) Maybe women know they'll be paid less so they don't go into tech to start with. It's kind of a chicken and egg problem.
b) As you've identified, because of so few women in tech, individuals who end up in well paid positions by chance are less likely to be women as well. So it's a statistical explanation in way.
c) There is sexism. I've seen it, together with xenophobia and other prejudices. And because of that women are rejected, as in not getting offers to start with, or even if hired not taken seriously.
d) In order to fix 2) women were hired but they didn't have an equivalent skill set or experience as men, so they got the job, perhaps to fill some diversity metric, but they did worse in performance reviews later on so they get a smaller salary, less bonuses etc.
Regarding d), I remember going out of the way to bring more women for onsite interviews trying to "fix" 2), that is I wanted to provide more opportunities for success and wanted to increase the diversity in the office. Most of the women failed the interview. I am sure c) was a contributing factor in some cases why the higher ups rejected them. But many simply didn't have their skill set at the level we were looking for. Had they've been offered and taken the job, they might found themselves in the position of getting a smaller salary and poor performance reviews down the road.
Now this doesn't present any good solutions, and doesn't address the lawsuit at hand because I don't know enough details about it. So it is mostly a breakdown of the issue as I see and from personal experience, as I was in charge of recruiting and interviewing for a good number of years.