The problem, to me, is that today at least in the US there are a lot of areas where there are truths to criticisms, but then the response to it is gratuitous and equally problematic.
This article struck me sort of similarly. Reason is an outlet I have a certain amount of respect for in general, but this article came across to me as more politically over the top in a way that the outgoing EIC's writing ever did. They would have done more good by simply highlighting the actual state of medical gender intervention research and leaving at that (it sounds like they have done this in fact, but they would have been better off as such). Even then it's complicated — I have friends who work in the field, and when faced with things like the Cass report basically point out that evidence of intervention effect or absence of an effect isn't the same thing as what decision will reduce harm the most in individual cases, and there's a lot of misconceptions about what's actually involved in gender-focused interventions. What's lost in these discussions is that medical care is not the same as science per se, it's about optimizing utility functions or something for individuals.
At some level this sort of critique over the Scientific American editor covering political topics seems a little precious and disingenuous. As others have pointed out, science has and always will be political, whether people want to admit those leanings or not. Pretending that it's somehow "above" politics is disingenuous and narcissistic, and leads to exactly the sorts of problems the author claims to care about. These more political topics have also become mainstream in science in general, and it would be a bit weird for an EIC at someplace like Scientific American to just pretend the discussions aren't happening. Is she guilty of bad writing? Maybe, but it is meant to be a popular science publication, and rants like this hardly seem like an appropriate response to bad writing.