Indeed, it always tickles me that defenders of the faith seem to enjoy twisting themselves into knots of Gordian proportion on the Flood's global nature, totally forgetting that in comparison to the genocide aspect, it's hair-splittingly irrelevant.
At the age of five, Skagra decided emphatically that God did not exist. This revelation tends to make most people in the universe who have it react in one of two ways - with relief or with despair. Only Skagra responded to it by thinking, 'Wait a second. That means there's a situation vacant.'