Of course it makes sense. At least inasmuch as pretty much anything in the Trek universe makes sense, yeah. He comes from the original timeline and had failed to prevent the destruction of Romulus. The Red Matter black hole sucks him inside and deposits him 129 years into the past, right into an altered history. Spock Prime is our connection to classic Trek and the universe we watched unfold for almost forty years and he's the evidence that the old timeline still exists.
Our revered Trek Classic didn't die, they're just not telling new, filmed stories in it.