I think this is reference to God's Creation. You see, the writer created both stories and was asked which one he preferred. And so it goes with God. He creates a number of stories, and the one he prefers is the story that plays out as history.

It is a conversational discourse with reference. First, what does the "it" refer to? "It" means the "the one with the tiger" and "the one" refers to the "the story (with the tiger)". Second, "and so" is a conclusion linking. THAT IS, the story of the tiger goes with God. Third, what does "God" here mean? It may not literally mean God, but a reference to religion in contrast of reason. In fact, the life of Pi has been struggled between his father's rationalism, with science and his mother's religion, with God, whatever in Hindism, Islamism or Christian. The sea cruise is an ordeal choice of Pi's belief, Science or God, for survival. You can make your choice after watching the movie, by choosing which story you prefer. Well, there has already been a choice given by Director Lee in the movie.