Yet we don't know what jobs women and men do at Google. There can be bias elsewhere in the system. For example women might be disproportionately hired as administrative assistants and men might be disproportionately hired as senior engineers. Both groups could then be compensated fairly and it would result in men receiving a disproportionately higher percentage of the money.
You've missed the point entirely. The comparisons are among peers in the same jobs. But it sounds like Google can't get its own data together in a sensible way, so you can't really trust any numbers in this article.