This confuses me.

In today's society, we often sex our babies before they are even born, by looking for the genitals in the ultrasound. By week 20 or so, we've already labeled them as a boy or a girl - and thus, which pronouns we expect them to use.

And this is a strictly physical observation - a biological observation.

Now I think it's certainly fair to question whether we want to continue this practice. As is made clear in the Scientific American article you linked to, people do not fall neatly into the two buckets of male or female. And so the practice of sorting all babies into the categories of 'boy' or 'girl' might very well be better left in the past.

But the way we have been using pronouns historically is clearly based on physical, biological attributes, isn't it?

Does that make sense? Or why doesn't that make sense to you?