Let me put it this way. What we're looking at is a terrible ending, not a Mass Effect 3 level of horrible, but a case where a bunch of writers who couldn't think of what to do decided to resort to the laziest possible way of trying to be profound: that is the creation of an infinite paradox. In the final equasion a lot of questions here can't be answered, which is kind of the point, it generates a lot of discussion for the point of discussion, and we see it every time someone does something generally good up until this kind of a lazy ending. As far as fandom goes we've more or less
been here with things like "Lost" before.
Indeed the nature of the ending seemed to have been leaked before the game came out, because I seem to remember hearing what the "infinite" subtitle meant before it even came out.
Your absolutly correct though, that by it's own intristic logic there would be a lot of cases where Booker was baptized but wasn't quite the same person he was when it broke down into the "sides" as we know them. Heck there would logically be dimensions where his baptism was a good thing, and "Comstock" was an outright benevolent figure. In the scope of this game it would be sort of like DC's parallel universe where Superman is a villain, and Lex Luthor is the world's greatest hero, etc...
That said, I'd imagine some of these questions are inherantly being held off for DLC. It's important to note that "Bioshock: Infinite", is not a complete game. Tons of DLC rounding it out was planned right from the beginning, this game getting attention due to being a high profile release that was also trying to get people to pre-order the DLC.
I sort of suspect that half the point of the lazy ending and all the "questions" and logical faults present within it, is specifically to get people to buy the DLC in hopes that they will clarify things and come up with a more solid ending.
That said as far as quality and pretty much everything up until the ending Bioshock is a pretty damn good game, my biggest concern (Elizabeth as a companion) was dispelled early, and it's probably going to set a standard as to what AI companion characters should be from here on if nothing else. Despite it's incredibly high reviews I am sort of wondering how well the game will fare reputation wise a few years after it's final DLC is released. Speaking for myself I think the original "Bioshock" was better because love it or hate it, it's storyline and reveals all wrapped up nicely, there wasn't the same kind of discussion along the lines "yeah well, I get what they are saying, but if that follows wouldn't this mean that this and that other thing are by definition true, which makes their entire ending and it's logic questionable" for weeks after it's release.