In the alternate reality Ben is a teacher of European history.
We can see that the island is now underwater, and depending on when it sank, chances are Ben had never visited it in this reality. Remember that he was not born on the island.
another possibility, when the incident took place, all nonessential personelle had been evacuated by sub, this included women and children. Ben may have been on the sub when it left.
Another perspective: We don't know that the bomb is the reason for the island sinking. Maybe something else that hasn't been revealed sank it.