having the freeze tableau, rather than the thwarting of the bomb plot, be the climax of the film. The ending opened up a beautiful world of possibilities with an endlessly cascading series of Stevens being able to communicate to each other across countless realities that "everything will be okay;" an idea perfectly crystallized in the image of the "Bean" sculpture at the end

The fascinating thing about the film is that it does not really explicitly state what the source code is doing, but if you understand it in certain ways, it is pretty neatly self-consistent.
In the lack of a clear explanation, I would disagree with the analysis above as to what the source code is doing. I agree with the idea of alternate branching realities as a consequence of a quantum mechanical view of time and action. However, I do not believe source code is “creating” any realities. I think of the time tracks as this film presents them as a nest of wound and jumbled wires, like in a junction box, except there are infinite numbers of wires looping in and around, and there is no concern about “filling up space,” so that an infinite number of wires can be jammed together.
What you called Timeline A above is just one of those wires. Given all the infinite possibilities of choices that could have been made throughout the history of the universe, it is pretty much guaranteed that, for any point on Timeline A, there will be an uncountable number of timelines running “next” to Timeline A, but in those timelines, the events on the train are happening. Seems unlikely? Remember that infinity is a lot. Even if there were a billion billion billion billion billion other timelines (and infinity is well more than that), and only 0.0001% of them met the criteria of running adjacent to Timeline A at a given moment when Stevens is to be sent, that would still be over a billion billion billion possibilities. One of the criteria is that the world developed more slowly by a few hours (however long between when the train in Timeline A explodes and when Stevens is to be sent). So here is what I think source code is doing.
The technology exists to project a consciousness from one quantum reality track to another, through the “quantum foam” that exists at the subatomic level (as long as the recipient and the person whose consciousness is to be projected are “compatible”). What the source code does is, using Sean Fentress’ perceptions, it can search the parameters of adjacent quantum timelines until it finds one which matches the criteria having the train running at that moment, and having the bomb on it, and meeting any other important criteria that can be gleaned from Sean’s consciousness. It then projects Stevens into that reality from the point Sean last remembers, eight minutes before his death.
In that way, no one is creating a “new reality.” They are putting his consciousness into a reality that already exists, as full and complete as our own. He can alter that any way he wants. Now, why do they insist then that he can only stay eight minutes? There are two possibilities: Rutledge does not understand the implications of what he has developed (unlikely), or he uses the veil of “you wouldn’t understand” to shield Stevens (and Goodwin, to a degree) from asking uncomfortable questions. He does not want Stevens to know that they are choosing to bring him back after eight minutes, even if he does not die in the explosion (or some other way); and that, if they didn’t, he could do exactly what he does at the end when they finally do let go of his consciousness: just get off the train at the next stop and walk into his new life as “Sean Fentress.” Rutledge needs Stevens to believe there is no other reasonable alternative.
Just look at how defensive and upset Rutledge gets any time someone questions him. He knows what he is doing, and what some of his underlings (and Stevens) would think of him if they knew as much as he did.
So, each time Stevens gets sent, it is into a different, already running and fully formed reality timeline which happens to have the critical moments passing adjacent to our timeline (in a quantum sense) at the moment Stevens’ consciousness is being sent. And when he is disconnected at the end, and they cannot bring his consciousness back, he goes off into a new life. The beautiful thing about the ending is that there is also a source code project in that reality (because it is so close to our own), and Stevens is able to get a message to that reality’s Goodwin to tell that reality’s Stevens that “it will be okay” — a repeated line and perhaps the philosophical crux of the film. I could easily imagine that Stevens then going into a different reality and doing the same thing, and so on, and so on, spreading out like a ripple into the water, spreading the message to countless realities in an endless, lovely string. This idea is captured visually by the perfect image of “The Bean” in Chicago. It is a gorgeous ending.
The only niggling point here is “what happens to Sean Fentress?” Clearly, Stevens does not carry any of Sean’s knowledge (and who knows what will happen if he tries to teach a history class). He appears as Sean, clearly, but where does Sean go? Goodwin at one point cryptically says “he is, for all intents and purposes, you,” notably saying “he is you” rather than “you are him.” Perhaps Sean’s consciousness does not even realize anything has happened. But I am not sure. In all this, alternate-reality Sean (actually, all of them) get the short end of the stick.