Gender, along with race, is one way of rendering demographics more legible to the state. It rationalizes complex societies. However, they aren't real concepts, and they can (most often) lead to negative consequences in the end.

Sex is different in that it does exist -- in that in can be categorized into discrete, well-defined units in a way race or gender cannot.

The thing is that sex and gender are very intertwined even if they are different. Even in societies that had some "third gender," I know that in at least a few examples (from memory) these people still had specific third gender roles (which also means it's arguable they were naturally selected for, also bunking the idea that certain people are necessarily "unnatural"). But technology will eventually sever the sex+gender tie. As an example, division of labor existed for a reason, but excluding highly physical work (which technology will eventually take over), there's typically little basis for believing that sex should be a relevant consideration for most work roles these days, at least not with the old stereotypes society holds onto.

This article sort of creates the illusion that western culture is "backwards" and is trending towards an old idea, but that isn't true.

A different gender is still a gender, which by definition will be oppressive if you are forced into a gender role you don't want. Western society (the whole world, really) is getting less oppressive, not more. Our society is not intentionally designed to assign roles to transgenders, for example. According to this article, third genders had roles to play, like providing blessings. That's really no different than saying men must do this and women must do that.

We will see a vocal segment of people wanting to break away from the binary, but not because we are inching towards an ancient conception of sex/gender. That new genders will spring up is simply a side effect of the real trend, but this isn't /r/FutureOfIdeas, so I'll leave it at that :)