I agree with all of this and wanted to make 3 points, some of which are echoing CiaoBob.
1) It is the best meal I've had in LA, period. I've only gone once, both because of cost, time, and just the fact that I want to try other places. But I will return soon. I love it, regardless of the genitals of the cook.
2) Chef's Table is not purely about food. Virtually every episode focuses substantially on personal life and obstacles the person in question has overcome. The point is to give you a window into the personal lives of the people who deliver such special food, so you know where this kind of thing comes from. Does this concept really need explaining? In the case of Ms. Nakiyama, her story of overcoming prejudice is unique both because of the history of anti-female bias in the Japanese cooking world, and a family member (her brother) who appeared to be actively rooting for her to fail in order to keep that structural bias in place. I found the story really interesting, as did everyone I've ever heard comment on it other than Aesthete.
3) The first time I went to Tokyo, I did something kind of touristy. I went on this walking tour of the city hosted by a Tokyo local who had gone to college at UCLA and then lived in the U.S. for a couple of years. The tour was great. Toward the end of the day, over a drink, the group got to talking about sushi and sushi culture in Japan. One woman, from Australia, asked why there were so few female sushi chefs. From there, we got a long history on how difficult it has been for women to break into the industry, including for (scientifically false) reasons like their hands warming the rice. In short, men have worked hard to keep it a male-dominated industry, and have propagated myths to keep women out. Long story short: it was not women, or Niki, who decided the genitals of the chef should matter. It was Japanese men. In that context, her success despite being a woman is highly relevant.
As Anthony Bourdain will tell you, food is about more than ingredients and technique. Sometimes it can give you a window into a culture. Kaiseki in particular is steeped in Japanese culture, and the fact that a woman is doing it allows a more interesting story about gender inequality in Japan. Like you, I am horrified by the story and background--but for different reasons apparently.