Hmm I suppose its not often someone is left alive after targeted in VATS. I thought he appeared instantly after confirming the action though?
I used to take the perk all the time in Fallout 3. He rarely shows up, I remember reading in the guide for Fallout 3 that you have a 10% chance of him showing up IF you fail to kill a target in VATS.
What happens is this guy in a trench coat and a pre-war hat has the mysterious magnum music playing and he fires a full load of shots out of his .44 magnum. The perk was useful against Super Mutant Overlords because those svckers were so hard to kill, but not even the mysterious stranger would kill them sometimes.