"Maybe, but I didn't start by calling you a liar just for mentioning them," And there you have it; you want to be right, start by being right. Shepard doesn't have the first idea what a thread array or golden formation of spirits is, but she figures that if it ever becomes relevant she'll figure it out. And if they're not real?

Well, other people's religion isn't really her problem, now is it?

"Got any more smart comments? Because I don't have to be your friend if this is how it's gonna be with you."

She doesn't like being called a liar, you see. A lot of people have died because she wasn't believed in time, despite her best efforts to the contrary.