I don't think the article inappropriatly conflates intersex and trans issues. I think that does happen a lot, so it becomes a sensitive issue.
But to me this article is making a fairly technical argument, both from a medical and legal perspective. Where she talks about trans persons it is because the specific argument or legal issue would apply to both - there are some overlaps in the issues around how we define "woman" for the purpose of sport.
As well, I think questions around the trans angle, which have become political in a way that intersex conditions never really were, have probably resulted in some of the lack of clarity in the public discussion around this. I really think the media's tendency to simply accept at face value the statement that she is female, and their hesitance to talk about the fact that she is XY, or has testes, is down to the trans advocacy movement, not intersex considerations. A certain group of people are convinced that they have to support XY men who transition as being really women, and there is a lot of political will behind it at the moment, so the sporting bodies have chosen to allow that. They know darn well what having men in women's sport would do, so they also have to try and mitigate it somehow through regulating hormone levels. Who knows, if they were only talking about making decisions about intersex athletes, if they would take some other approach. It's all being defined by what is politically possible around trans issues. So I think it's probably impossible for the author to avoid talking about it.
As far as athletes and the level playing field - I agree that seems like it ought to be true, but for some reason, in elite sports it isn't. Part is of course pressures from sponsors, governments, but I think there is more to it than that. Something about that culture can go a little wrong somehow, maybe it's just something extremely competitive people are at risk for? Or something about the way training psychology is approached?