I'll start with the fact that the whole project relies almost entirely on a very large assumption: prayer works. The overwhelming majority of studies that have looked into whether prayer has an effect or not have reach the same negative conclusion. Prayer does not work. Not only does it not work there is no reason to believe that it can work. The only "evidence" advocates can come up with is anecdotal. Until a body of evidence emerges to support the claim that prayer works there is no basis from which Mawson or Brierley can draw any substantial conclusions.
Even setting aside such a fundamental flaw as the assumption that prayer workers there is another glaring defect in the project. It is an innate contradiction. It is not even remotely possible to run as an experiment. Mawson does make a few feeble attempts at getting around this but fails completely. The simple truth is that by definition an atheist cannot "pray." So there can be no misunderstanding, it should be pointed out what the actual definition of prayer is. According to the Penguin English Dictionary a prayer is, "a personal request, confession, or expression of praise or thanksgiving, addressed to God or a god." Think about it for a minute and then ask how is it possible to pray to entity you have no belief in. To further get a sense of just how ridiculous of a premise this is replace God with any other figure you do not have a belief in. It would end up sounding something like, "Of great Wizard of Oz please make me believe in the Wizard of Oz." Prayer cannot work even theoretically unless you already have a belief in its efficacy which would then require a belief in God. By definition anyone who genuinely prays cannot by definition also be an atheist. This is not an example of the "True Scotsman" fallacy since it is the established definitions that make it a contradiction. It is rather an example of trying to claim something along the lines of a square simultaneously being a circle. The conditions rather than the interpretation make it impossible to be reconciled.
So what's the point? I have no idea. At least, not when it comes to those atheists who have chosen to participate. It sounds like some are hoping to get a few Christians to finally concede that prayer doesn't work or to get them to stop pestering us about our supposed lack of understanding. I wouldn't hold my breath on either. Those who insist of prayer efficacy will find a way to blame us for their own failed notions. They always do. As for Brierley and his group, I have a sneaking suspicion that this is more about PR than any possible results. It would not surprise me if a few of the "atheist" participants are not in fact atheists. I have no reason to doubt Seidensticker but he can be duped and already gave a few hints that he has already been suckered. He makes a reference to Leah Libresco in his initial post on his joining the project that I find a bit foolish. She was not an atheist. Reading her early blog posts should make that point pretty well.
I will be following his updates on this project. I fail to see how it can be anything but waste of time but I suppose it could be amusing if nothing else.