I'm having a hard time envisioning why the engine would care if you shut the bike down with the kill switch or the ignition switch.

While the engine is running, it tends to load the mounts slightly even at idle. When you shut it off, the load is eliminated and things tend to move slightly. If you have a mechanical clunk, try watching at each mount while someone shuts the bike down to see if you can observe any movement that could result in your noise. Check for looseness where the stabilizer links attach to the frame and the engine, and where the link brackets attach to the engine and frame. Don't forget the exhaust system. If you eliminate all the external possibilities, it's probably just a little backlash internally on that last compression stroke which could make the compensator or other parts give you a little clunk. Since so many seem to have the exact same thing, it will most likely be one of those "normal" things from the all time leader in "they all do that", Harley-Davidson. If it doesn't blow up, it's good.
Jerry