I have two arguments for going for Box B. First, for a scientist it’s not unusual that every rational argument (=theory) predicts that only two-boxing makes sense. Still, if the experiment again and again refutes that, it’s obviously the theory that’s wrong and there’s obviously something more to reality than that which fueled the theories. Actually, we even see dilemmas like Newcomb’s in the contextuality of quantum measurements. Measurement tops rationality or theory, every time. That’s why science is successful and philosophy is not.
Second, there’s no question I choose box B. Either I get the million $ -- or I have proven an extragalactical superintelligence wrong. How cool is that? 1000$? Have you looked at the exchange rates lately?
I wonder if anyone ever remarked on the seemingly excellent evidence thus provided for Hinduism over Christianity. Probably not.
Well, David Hume did. In the Dialogues Concerning Natural Religion. Although not with a totally straight face.
The best book-long treatise about your points is probably Dawkins’ The Selfish Gene. But you probably know that.