I think the magical appearance theory is little suspicious. Why Hogsmeade? Why not other shops like Three Broomsticks? Besides, if ROR can make a tunnel up to Hogsmeade on its own, it can make tunnels to anywhere possible. Why then, it did not help Harry escape during HP5, Umbridge's ambush?
I have an alternate theory. I think the passageway was created by Dumbledore during HP3.
You remember the story Dumbledore told the group of 13 during Christmas? That he found the ROR while going to the bathroom? Well, he did not elaborate on that. But I think a curious man like Dumbledore is unlikely to just flush and leave the toilet. He surely discovered the full secret of ROR then.
Now during the events of HP3, Dumlbedore was furious about Dementors guarding every entrances of Hogwarts. I think he understood how vulnerable Hogwarts is at that point. I am not saying he foresaw the exact future of HP7 that time. But Dumbledore obviously is a man who does not like to be trapped. Besides, he made plans for every possibilities. After discovery of ROR, I think he formed a plan to make an escape route in case Demantors go out of hand. Whether he dug the tunnel or asked Abeforth to dig it, cannot say.