Just had a discussion with my friend who also completed the game to completely make sense of the ending.
Booker in all realities committed atrocities as highlighted by visiting the Battle of Wounded Knee and the Chinese exhibits. There, Booker and Slate slaughtered many Native Americans and Chinese people, so they have both sinned by killing minorities.
These events afterward are where Booker divides the world to two.
Booker A does not baptize himself and lives life normally. Has Anna. No Comstock. No debt.
Booker B baptizes and goes on his crazy journey to become Comstock aka the prophet and leads Columbia to secede the union. The Luteces, crazy quantum physicists, introduce time tear to Comstock to make people into believers that he is the prophet. However, doing so makes Comstock age quickly and now Comstock cannot fulfill his ultimate dream of ruling the world because he's infertile due to his age. He would need an heir to fulfill his duty.
Luteces play with time tears and find that Booker A can have a child. Using time tear, they somehow mess with Booker A's timeline that he would need to give up Anna to pay off his debt. Anna is brought in to Booker B's aka Comstock. Comstock now has an heir, and he can die because Anna will fulfill his duty.
Because of the idea of infinite possibilities, one of the events possible is that Comstock who used the Luteces to bring in Anna is that he goes on to kill the Luteces "in an accident" in order to prevent a correction in the timeline. However, this operation fails and creates multiple realities timeline which then these crazy physicists use this phenomenon as an experiment to bring each other back. Booker B then senses the Luteces upheaval plan and warns his believers about the false shepherd, and his coming will destroy the lamb (his heir).
Knowing about time tears and feeling bad about taking away Anna in the first place, male Lutece wants to do right by time tearing to Booker A's altered timeline post no Anna that he must bring the girl back to New York alive to prevent Booker B's endgame. Female Lutece disagrees but grudgingly goes with what her brother wants. Luteces experiment which Booker would successfully avoid the world apocalypse. However, in all trials, Booker A chooses the same results even if he is told the results beforehand (e.g. coin flip always heads tallies on chalkboard, Ball #77 from telegram), and the world ends the same. They are trying to see what variable they can change to prevent Booker B's end game come true.
Anna in all these events becomes a time god and sees that the only resolution to this is to destroy the event when Booker B chose baptism. This is the story's ending assumption and why some people are having problem with the story. Because Booker B chose baptism, and that baptism opens the road to making Booker B to becoming Comstock, there remains that one possibility that Booker B wants to kill the Luteces which then repeats the events that the Luteces experiment with Booker A's in different variables.
By eliminating the chance of Booker B's possibility, only Booker A will exist, which is what the ending + post credits suggest. No Booker B. No Comstock. No Lutece.
Whatever. Maybe my friend and I are crazy, but this to us seems like a "logical" ending.