Frank's point got rather lost in all this. It seems to be quite simple: there's a warm fuzziness to life that science just doesn't seem to get, and some religious artwork touches on and stimulates this warm fuzziness, and hence is of value.1 Moreover, understanding this point seems rather important to being able to spread an ideology.
The main problem is viewing this warm fuzziness as a "mystery." This warm fuzziness, as an experience, is a reality. It's part of that set of things that doesn't go away no matter what you say or think about them. Women (or men) will still be alluring, food will still be delicious, and Michaelangelo's David will still be beautiful, no matter how well you describe these phenomenon. The view that shattering mysteries reduces their value is very much a result of religion trying to protect itself. EY is probably correct that science will one day destroy this mystery as it has so many others, but because it is an "experience we can't clearly describe" rather than an actual "mystery," the experience will remain. The argument is with the description, not the experience; the experience is real, and experiences of its nature are totally desirable.
The second, sub-point: Frank thinks that certain religious stories and artwork may be of artistic value. The selection of the story of Job is unfortunate, but both speakers value it for the same reason: its truth. One sees it as true (and inspiring) and likes it, the other sees it as false (and insidious) and hates it. I think both agree that if you put it on the shelf next to Tolkien, and rational atheists still buy it and enjoy it, hey, good for Job. And if not, well, throw it out with the rest of the trash.
Frank also has a point about rationality not being the only way to view the world. I think he's once again right, he's just really, tragically bad at expressing his point without borrowing heavily from religion. His point seems to be that rationality isn't the only way to *experience* the world, which is absolutely, 100% right. You don't experience the world through rationality. You experience it through your senses and the qualia of consciousness. Rationality is how you figure out what's going on, or what's going to be going on, or what causes one thing to happen and not another. Appreciating art, or food, or sex, or life is not generally done by applying rationality. Rationality is extremely useful for figuring out how to get these things we like, or even figure out what things we should like, but it doesn't factor into the qualitative experience of those things in most cases. For many people it probably doesn't factor into the enjoyment of anything. If you don't embrace and explain this distinction, you come out looking like Spock.
This seems to be a key point atheists fail to communicate, because it is logically irrelevant to the truth of their propositions. A lot of people avoid decisions that they believe will destroy everything that makes them happy, and I'm not sure we can blame them. It's important to explain that you can still have all kinds of warm fuzziness, and, even better, you can be really confident it's well-founded and avoid abysmal epistemology, too! Instead, the atheist tries to defeat some weird, religiously-motivated expression of warm fuzziness, and that becomes the debate, and people like their fuzzies.
We experience warm fuzziness directly,2 through however our brains work. No amount of science is likely to change that, no matter how well it understands the phenomenon. This is a good thing for science, and it's a good thing for warmth and fuzziness.
1- I have admittedly not read his book. It's quite possible he's advocating we actually go through religion and make it fit our current sensibilities, then take it as uber-fiction. If that's the case, I have serious problems with it. If that's not the case, and he just thinks that some of it contains truth/beauty/is salvagable as literature, then I have serious problems with the argumentum-ad-hitlerum employed against him, as it seems to burn a straw man.
2 - I'm not saying there's warm fuzziness in the territory and we put it in our map. There's something in the territory that, when we map it out, the mapping causes us to directly experience a feeling of warm fuzziness.