Actually, if you watch the ending again all the Elizabeth's disappear but one.
I beat the game late last night so I still haven't time to process everything but I think if someone comes up with a chronological timeline it would help immensely. From what I remember, it seems like the following events preceded Columbia seceding from the USA:
4. Racked with guilt over his past sins he seeks forgiveness through baptism. (note: I don't know what sect of Christianity baptized him but I've never heard of someone taking a new last name in baptism - only a new first name. It would make sense if later he officially changed his last name to Comstock in an effort to distance himself from his past but I think having him change his full name at the baptism was done for storyline reasons (at that moment he became Zachary Comstock) rather than accuracy.
5. Some time afterwards Comstock is visited by an angel (was this just a delusion of his or something he viewed from a tear?) which causes him to reject Christianity and start a new religion in his own name.
The last note implies that our Elizabeth disappears off screen. All the other disappearances correspond with the piano notes. There's no one left to disappear by the end except our Elizabeth.
4. The name changing goes along with the theme of rebirth. People try to change their names all the time to become a new person. It's a way to leave their past behind.
5. Comstock was never visited by an angel. Most religious figures have some sort of divine meeting in his origin story. Comstock made up his. It's been a common practice throughout human history. Often, whether someone believes a religion is real or not, depends on whether a person believes in its origin stories. He's not rejecting Christianity. He's co-opting it and creating a new sect.
On the question brought up about causality. Yes, I don't think many writers ever adhere to causality, because that would make the story frustratingly static.
On the connection between Rapture and Columbia, I think Levine threw that in there just to mind fuck the players. I don't think DeWitt and Jack are analogs. They do not have similar themes. Andrew Ryan and Comstock have somewhat similar themes, but only because all villains usually have some delusions of grandeur, don't they?
Not to mention, that, since they all spring from the mind of Levine,they will have some surface similarities. Also, being a game, we almost always have to have a hero character and a villain, don't we?