In Walgreens and Walmart, that WAS the case for years as negotiating a salary was the employee's problem (up to 2006 for Walgreens), but lawsuits 'changed' that in both cases. That's kind of why at least Walgreens and Walmart finally adopted a scale salary like the rest of the companies. Before, you used to have to negotiate those matters with the RxS. A scale salary doesn't mean that everyone in a market is paid the same, but the salaries are explainable by a neutral party when arbitration needs to happen.
For the federal government, there is actually still both a salary and pay imbalance between men and women, but not when you take into account the rank structures as the OPM mandates and regulates pay and raise benefits. If compared without qualification, men do actually make more than women. When compared rank by rank and step by step, the salaries are equal, but men still are paid more due to OT differences. But at the rank structure, men hold many more of the senior ranks (GS-14 and up to SES) than women even adjusting for the age and experience gaps. The distributions for the SES pharmacists within the federal government (all twenty-eight federalwide) are predominantly men (as in 4 F to 24 M and none of the 4 F just have PharmD as a qualification while there are actually BS, RPh's among the men). Same with GS-15 (Chief/Director grade) and GS-14 (Deputy Director grade) which are also predominantly men (don't have the OPM numbers in front of me). There's still considered to be a promotion differential not in favor of women pharmacists considering the demographics in the civil service, and whether it's due to lifestyle choices (that's one explanation), network effects of guys hire guys (that's another explanation), simple gender discrimination (that's another explanation), or the lack of time are satisfying explanations even in part.
I don't hold the belief that in our generation, that there will be an institutional problem with the FDA, NIH, or VA having their Chief Pharmacist, Title 42 NIH Senior Investigator, and Chief Consultants be women. However, I know enough of the Boomers and X'ers in those positions right now to know that some of them have more regressive beliefs that they know better than to air in public. And then there is NIH, which still has a quite sizable group (thankfully in the older generations) that is openly misogynistic that we are just waiting them out until their death or retirement which I feel very confident that despite the measures taken have impeded good science from being done.