The quick twitch of a gunslinger's gun arm could easily be described as a burst of energy.
Again, he was still able to walk over and shoot him again. THAT describes exactly NOT a Golden Gun.
English
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"Two shots. Two bullets engulfed in an angry glow." Shin fired two shots at Yor before walking over to him. A Golden Gun has three shots.
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And since when does it take 3 shots to kill a guardian?
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You're forgetting that Dredgen Yor wasn't a Guardian anymore. He was wielding the power of the Darkness. That could have made him withstand the first shot. Also, how do we know he didn't die from the first shot? It seems like Yor was manipulating Shin, in a "join the Dark side" kind of move. Shin was perhaps provoked to fire out of rage and then most likely shot Yor more times than necessary.
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Again, enemies are vaporized by gg. That's how we know.
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Like I said, Yor was not an ordinary Guardian. Actually, he wasn't a Guardian at all, he was powered by the Darkness. With those powers, he would have easily survived the first two shots. But you're forgetting something. Since when did gameplay affect the Grimoire? You're basing everything you say on the idea that gameplay mechanics would affect the lore. Lore can affect gameplay, not the other way around.