Just reading the article, the guy is exploiting ai, reloading multiple times to reverse pickpocket guys, using mines on bosses until their health is low enough and getting other npcs to kill them and farms experience for countless hours making settlements.
The guy who did it even says that a pacifism run clearly wasn't meant to be possible and wonders why it's so hard in this fallout. Even Todd Howard didn't think it was possible.
From the article:
"The entire thing is a test of patience. The run makes ample use of save scumming, that is, the practice of saving before taking an important action and then reloading if it fails. Fallout 4 has a perk called “Wasteland Whisperer” which lets the player pacify enemies—instead of attacking the player, the enemy will simply put their hands up. However, having the perk doesn’t guarantee it’ll work. It just gives you a chance of calming down your enemies, and Hinckley can’t rely on a dice roll to complete the game with zero kills. So he reloads and tries, tries again, until it actually goes through.
It’s a brute-force method, yes. Like I said earlier, Fallout 4 really doesn’t want you to play the game this way, and all of its mechanics ensure that, at some point during a normal playthrough, you’ll have to lodge bullets into someone’s noggin. Even if you take the so-called peaceful perks."
’I can’t tell you that you can play the whole game without violence – that’s not necessarily a goal of ours,’ Howard told The Guardian.”
In fallout 1 I literally beat the game with a character at level 7 who used sneak, speech and outdoorsman as tag skills and never used a weapon and managed to talk my way through encounters, without killing, and it was designed to be able to be done that way. No game exploits or anything. There's a big difference from an RPG being designed to play numerous different ways, one being a pacifist, and somebody glitching and exploiting a game to be able to do it.