Is there any evidence that this is what actually happens? Are all women carrying around these stereotypes with them? It just seems like a "just so" explanation.

Most of the examples in this article aren't of stereotype threat, they're examples of the authors' insecurity and social anxiety about being in tech. I can understand how a women would feel uncomfortable working in large groups of, what are generally socially inept, geeks but that seems like a different problem. This was the money-quote for me:

I remember one instance in particular when I was feeling particularly isolated at our company. “I feel like an outsider! Like the guys don’t want me here because I’m a woman!” I whined to one of my male colleagues. He looked at me and replied, “Well that’s dumb. Of course they want you here. You’re great to work with.”

So essentially this woman has a self-confidence issue. I see little evidence from this article (and the NPR one) that these problems, to the extent that they exist, are just run-of-the-mill social anxiety and nothing more.