I really don't understand how drowning Booker Dewitt would prevent Comstock from ever existing. I have thought about it and it just isn't logical. Here is my understanding of the timeline:
Booker Dewitt, who I will refer to as Booker 1.0, is in the battle of Wounded Knee. Booker 1.0 does some horrible things and has a hard time coping with them.
Booker 1.0 then goes to the place to get baptized. But since the baptism leads to a choice he can no longer remain Booker 1.0. This produces a Booker 1.1, the one who doesn't get baptized and a Booker 1.2, who is baptized and becomes Comstock.
So Booker 1.1 gets married and has a child. Booker 1.1's wife dies during the birth of Annabelle Dewitt. Booker 1.1's life sinks due to drinking and gambling. Booker 1.2 (Comstock) meets with Lutece and starts making his floating city. Booker 1.2 is unable to have children and plans to get Annabelle from Booker 1.1. Booker 1.1 eventually gives up Anabelle to Lutece to "wipe away the debt" and Annabelle ends up with Booker 1.2.
Twenty years later, according to Elizabeth/Annabelle, Lutece come for Booker 1.1 in the apartment that he has been living in. Lutece essentially give Booker 1.1 a chance to fix everything.
Booker defeats Comstock but Elizabeth tells him there are infinite version of Comstock, Booker 1.2X, out there. So they decide to "smother" Comstock. Ultimately many versions of Anabelle/Elizabeth drown Booker 1.1.
That is my understanding of the timeline. How does drowning Booker 1.1 prevent Booker 1.0 from going to the baptism?
A friend of mine told me that Booker 1.1 became Booker 1.0 when he entered that universe. I really don't think that is the case. If that were true, then Booker would have embodied Comstock when he entered his world. The entire game, till you kill Comstock, there are two Bookers present in every timeline that we experience. So why weren't there two Bookers at the baptism?
I enjoyed the story, but I feel this is a gaping plot hole that is keeping me from enjoying the ending. If I am missing something please fill me in. My understanding is the all the Lutece would have had to do to correct there mistake is killed Booker 1.0 before he went to the baptism and all branches from his story would have been cut off and non existant.