I don't miss anything.
The study you posted is just as valid as the ones I posted. I underlined a few sentences in the study to show the negative intention. The guy is bound up in scientism, and is not open to other possibilities as shown by the quote "which a rational scientist would expect". So we know that his expectation and intention were negative. He got what he expected, which is what prayer is. He's actually showing us that if you're negative, you will get a negative result. Then he goes on to say that prayer "can have negative consequences", which is quite laughable isn't it?! I mean the guy is hell bent on saying there's no effect at all and no higher power but then comes out and says there's a negative effect and that people should be very careful about. That's quite stupid on his part. To finish off, he shows his full on negative bias and intention by saying "there is a higher entity that would somehow take some time out giving children AIDS in Africa and cure their cancer". Can you see that there is a very bitter and disappointed guy talking?
As I have stated above prayer doesn't need a "God" to work; it's about consciousness + intent. If you want to throw in a God then that's fine by me. Intention is easy. Developing the necessary degree of consciousness is the hard part and that's why in most cases, and for most people, prayer is not going to work.
Sorry I should have pointed out after the quotes was my 'bitter' words not that of the study. Actually the study was carried out by the Templeton Foundation who's goal is the "progress in spiritual discoveries" so it's fair to say they hoped for different results especially when most their funding comes from numerous religious groups.
As I said prayer can only benefit as a placebo effect.