Well, I am a christian, and maybe in order to see how much Tool is not a christian band have have to be one.

There are references, but they are always narrative devices. He comes from a strongly christian household, so it's no surprise that even though he's not one the references make their way into his lyrics.

I've said this before, but why does everything sung have to be from a first-person perspective? Using christian symbolism in music is just the same as using any other symbolism, to me. And he's been doing it since way before 10K Days. They're on every album. Really, you don't have to look very hard.