He knew that John had no siblings, so that ruled out the idea that it was a twin. "A doppelganger. For some individuals, there exists another who looks completely like them. The cause is not known."
Alternate reality? It was a slight possibility.. a very slight one. He had files on how Skynet worked, and that wasn't one of them. Even the method of time travel wasn't perfect, as only living things can go back.
"Unknown. But there's is a 12.5 percent probability that it's possible.. though perhaps unlikely. There is no data to prove it one way or another."