Another alternate reality issue (spoiler)
Others already raised the point that Colter takes over Ferris' mind, body, life but that Ferris would be dead anyway if the bomb wasn't stopped.
Another issue (question from me) is Colter's original brain and body. In the alternate universe where Colter is in Ferris' body and the train is saved, the Source Code military base still exists. Colter's brain and body are still alive on the Source Code.
So is Colter's consciousness alive in both his dead mutilated body AND also alive in Ferris' body ?????