In my experience, the programmers who are particularly able to negotiate aggressively and are conflict-seeking achieve the goal of getting their designs adopted, which usually doesn't correlate with getting the best designs adopted. If you don't believe such a correlation exists, you get a more productive development team if you artificially avoid rewarding aggressive negotiation and self-advocacy. It's an important skill in other disciplines like sales (where the goal is to close the deal even if your company's product is unquestionably worse than the competitors' products), but not so much for engineering.

I also think this isn't so much "women aren't good at negotiating for themselves" as "women who negotiate for themselves aggressively and are conflict-seeking are penalized socially for non-womanlike-behavior, so they learn not to do so." There are legitimate criticisms to be made about implicitly buying into that social standard, but it seems like an easier change to just prioritize different things in compensation, if the goal is short-term fairness in compensation.