I understand how the baptism after Wounded Knee (1st baptism) is important. I'm completely lost on the significance of the baptism (by the same priest) that occurs when you first enter Columbia (2nd baptism). What does this 2nd baptism do? Why is he magically teleported to a different area of Columbia immediately after the 2nd baptism? Why did he say he was downed (or almost drowned) during the 2nd baptism? Why doesn't he turn into Comstock after accepting the 2nd baptism? Why was Booker taken directly from the lighthouse to a completely closed off section of Columbia where he is forced to accept the 2nd baptism to leave?

He is not teleported. He is either carried or floats there. And the second one did not change him because he had passed that point in his life where he was deep in despair. At the end you see that he makes up his own memories and forgets about the part about him selling his daughter ( is why he gets baptised and has a near death experience or brain damage from lack of air) So the second one is not as important in that regard.

For the lighthouse thing go look up Ellis Island. Its the same idea.

The reason for the Baptism is foreshadowing.