Honestly, there are some things that they both miss. The NYT article, I agree, didn't need to bring in trans-ness because it discredits her argument. I agree with the open letter, to a point. It would seem that the NYT article author didn't realize that she's actually making it easier and more justified for people to question the legitimacy of trans identities.
I agree with a few here that it is entirely possible for someone considered a tomboy to belong on the spectrum, but I wouldn't hold out for that to be any sort of conclusive argument. Honestly, every person in the world is on the spectrum; some just happen to be less of an extreme than others.
That being said, I've been attacked (CPS involvement and everything) by the community in which I live for allowing my son to dress the way he wants. He, at times, will wear dresses, earrings, fingernail polish, and many other things considered "girly". Do I question him about it? I have once, but I don't hound him about it. He likes typical boy things and typical girl things. Does he have to choose? Hell to the naw. I asked him whether he feels that he is a boy or girl and he just says, "I don't know," with a shrug. I showed him a chart of the gender spectrum and he pointed to somewhere in the middle. That's good enough for me. He still gets treated the same as before, with the same pronouns and name. If he feels differently and wants to be treated as such, I will make it happen for him. Until then, he can do what he likes. My point is that people need to keep their noses out of other people's business and stop trying to tell them how to live their lives.