If they don’t control most of the nodes in-between they can control all the exit nodes they want. If you connect though 3 Tor nodes, as soon as one of them is not controlled by them they likely can’t identify you.

That’s not to say that they don’t control most of the nodes, and your traffic likely goes through NSA nodes exclusively

“Czesc, I am Mister Anonymous. I would like to buy this Book. Please send it to Jan Pawel at this address, dziekuje.”

I am not sure what he’s hinting at. Just using Tor doesn’t bear any legal risks. Hosting an exit node is different, as depending on the country you might get into serious trouble if certain traffic goes through it.

You’re right on the spot with media reporting on this.

To be fair the vast majority of scientists will take other factors into account. If you thought of “this could also be because of that” then you can be sure that the scientists and the ones reviewing the publication also thought about it and addressed it. There are exceptions, sure, but don’t just assume everyone is bad at their job.