That is not as simple as you make it seem. First, you need a gun that shoots only bullet per trigger pull, not a burst or automatic. If you get more than one extra shot in after the NPC goes down, they're dead.Just carry a pistol and shoot limbs, it non lethal. There also the non lethal mod still in the game. This is just an issue of you not experimenting, as the feature is still live and well in game.
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Using PAX in weapons would be great... but weapons generally don't have an open mod slat until Tier 3 which first happened for me at level 21 while I was well into act 2.If you are accidentally shooting people in the head that is a skill issue. Use the pax mod. Iconic weapons usually come with mod attachments already baked in them, or/ and you can add scopes and muzzles.