When arguing with someone who holds some fantastic notion (e.g. "God only helps those who help themselves," as an answer to, "Why didn't your god answer my prayer?"), they tend to lament about how difficult it is to explain "deep spiritual truths" to the faithless skeptic. When this happens, it's best to be as empathetic as possible. Maybe it's difficult to explain because it's hard to make up sh!t on the spot, amirite?

I agree with the example that you included, but in general I actually do find it hard to explain God and religion in an argument, no matter how much knowledge I have on the topic at hand. It's not because I couldn't "make anything up" but because God and His actions will constantly be a mystery to everybody, not just those who don't believe in Him. So if a religious person is having a hard time in a debate or conversation or whatever, keep in mind that they have probably come up with their own questions and are trying to increase their own knowledge.