1. Specifically, Booker was drowned at the exact moment he had the ability to become Comstock. By negating the chance of Booker becoming Comstock several things in the continuum no longer occur, starting with Anna becoming Elizibeth, Columbia being founded, the hundred coin flips, everything that requires Columbia or Comstock to exist is forever nullified. Booker and his daughter however do still exist as evidenced after the credits (Fucking Aftercredit stingers!) but Anna never lost her finger, never gained the ability to fabricate Tears, and Booker never became Comstock. Comstock is gone, but so is Elizabeth as we knew her.
2. The underlying assumption is given by Liz at the end of the game, which is very similar to the series “Higurashi: When They Cry” where one character is transported to a new version of her town when she dies, this new world is mostly similar but there are key changes. One person may suddenly be a smoker, one may be clinically insane, waffles might always be on sale. Thus its *possible* that spiritually we have been playing Booker all along. Evidence is in the Luteces, who in their conversations always seem to purposefully be the polar opposite of what the other is saying “Living Lived, will Live/Dying, Died, will die”. This all strongly points to the possibility that the Luteces are the same person but due to the Space-Time Continuum were born different genders.
So Rapture was not exactly “moot”, Jack either saved or destroyed it, and the Big Daddy saved or destroyed it again. At the ends of their lives, Fate and Time reloaded the gun, spun the chambers, and thus the Comstock dilemma occurred. Bookers soul up to Infinite seemed doomed to explore failed utopias for the rest of space and time, a cycle presumably stopped by the Luteces. Or has it? All we know is that Columbia no longer exists, and time being so complex will inevitably be thrown out of whack again.
3. In my play-through, very little information on the Siphons was found so my knowledge on them is rather low. However I have observed that with the Siphons in place it forms as a “Block”, thus it stands to reason any location with a Siphon can neither be Teared out or into; and we can expect Comstock realizes this. As to why Elizabeth suddenly wishes for revenge, well, she begins to understand and remember that like Comstock she was created, not born. She understands that in order to break the cycle she needs to kill Comstock and destroy the Siphon to unleash her full energy over space and time. While there may be infinite universe, not all of them contained Comstock, just like not all Universes contained Rapture, only ones where Andrew Ryan was capable of building it. Thus by preventing Comstock from being created and killing Booker at that point in time she ensured that Columbia, Comstock, and by proxy her, were never created.