I don't think anyone has disputed that the ending as you typed is what happened. Colter created an alternate timeline for himself where he saved the train, disabled the bomb and got to live (one assumes) happily ever after with Christina.
It's because you misunderstood me.
He didn't create an alternate timeline. He jumped (traveled) into another universe (already existing).
The crippled scientist pretended Colter was only sent into the body of an already dead man (in our universe). He was lying.
The crippled scientist wanted somehow to hide that fact. Because, we can say, that scientist only cared about our universe and his success. He didn't mind what happened in other universes. Even if other universes are as real as ours (and not the creation of his machine through some form of time traveling).
But Colter was convinced the different universes (trains) he visited were real not a fabrication of the source code machine. He was right.
For example, as I said more explicitly in the other post, stopping at that freeze frame pictures don't make any sense considering that those people were not about to live their last seconds in any way. Nor was Colter or his girlfriend. (EDIT: Colter could have been dead by giving back the body to Shawn consciousness after the 8 mins, but the girl military changed that by pushing stop on the machine where dead Colter was laying in. So I guess that ending could still be very possible when I think about it)
Also it explain why having someone like Colter jumping into the mind of another person (supposedly dead) can able him to interact with that "universe" the body was. And "know" more about it than the mind you jumped into (Shawn).
Shawn didn't know who the bomber was. So why jumping into the memory of shawn last 8 mins able you to interact with the whole universe that persons was at? The cripped scientist was lying. It's not what is happening here. Colter was sent into the body of a man in another universe in which very similar events (99.9% similar), at
almost the same time, with the same criminal behind it, are
about to happens. There's an obvious time constraint here, as shown in the movie. No alternate timeline was created at all. Althought some catastrophic events were averted in 2 alternate universes and the bomber was stopped from doing more damage into our universe.