ACTUAL ANSWER: My guess is that it has to do with NLB's iron sights. Regular snipers have a holographic reticle, and its position on your screen and whether it overlaps the enemy's head edicts whether you get the kill or not. When you're flinched with a regular sniper, this dot and the rest of your screen will move, but if the dot overlaps with a target when you fire, you get a kill.

Unlike regular snipers, NLB has an iron sight. However, the tip of the iron triangle counts as its "reticle," and the game still treats this triangle as if it were the red dot sight on any other sniper. When you get flinched with NLB, the game treats the sights exactly the same as if it were a regular sniper, even though you can see the rest of the gun kick into your view when this happens. So regardless of the barrel's direction, if that triangle is visually overlapping with your target's head at the moment you pull the trigger, the game gives you the kill.

TL;DR The tip of NLB's iron sight is the only indicator of whether you get the kill, flinch or otherwise.