Having just finished "Darwin's Watch", I reckon Nation is a continuation of Darwin's Watch, but in fictional form. It is about someone who struggles with his belief in God and in the end, finally rejects the concept of a supreme being, choosing instead to place his faith in science and humanity (like I believe TP does).
"God (Imo) made as clever enough to work out he doesn't exist"
In Darwin's Watch, in the alternative trouser of time, Origin of Species is written 100 years later by Richard Dawkins. The same guy who wrote the excellent "God Delusion" - an argument against religion which was very controversial. What a coincidence, Richard Dawkins also pops up in the last chapter of Nation and is called that "nice professor Dawkins".
Darwin's Watch has a go at creationism which claims the world is only 6,000 years old, saying it's all nonsense. Nation has a lost civilisation from 30,000 years ago. QED Creationism is wrong.
The whole of Nation is littered with anti-God/religion statements.
When I started reading Nation the first time, I couldn't understand why it wasn't set on Discworld. It could have been a small island somewhere and an AM ship. If it was purely an anti-war/anti-kill/anti-hate story there would have been absolutely no reason why not.
But on Discworld Gods exist. There's hundreds of 'em. It had to be set somewhere where there was only ONE God ie; a trousers of time leg of roundworld.