There are a lot of problems with this article, it is clearly written by someone with an agenda, as it is lacking the usual caveats we scientists tend to work with.

Main problems:

1) The studies cited are not quite solid science. Take this quote:
"We see evidence for this in girls with a genetic condition called congenital adrenal hyperplasia, .."

For us to believe that testosterone leads to these preference differences, we have to believe that people treat girls with the condition equally to girls without. Otherwise we haven't gotten any closer at disentangling the nature vs nature argument. So this study can only suggest, but it proves nothing.

2) Imagine these studies are true. They say nothing about magnitude. It is quite the leap of faith to say that there are gender differences at birth, and then use this to claim that STEM should be naturally dominated by men. There could be very real gender differences, but this tells us nothing about how many more men should be in STEM.