Except in those cases it's even more important that the NPCs don't do anything unexpected. Those NPCs are like actors in a stage play, you don't want them to come up with their own lines and confusing the audience.
Don't forget there is a certain randomness with 'more natural' and with randomness you're going to invite Murphy to the party.
Not all NPCs have to be part of a script. They can just be additional characters that add life and realism to the simulated world.
A weapons maker with a unique backstory and realistic conversations that reference it is more interesting than a bot, and opens up the possibility of unscripted side-quests.
In many cases maybe. Personally I would love to play a game with a world inhabited by "individual" NPC AI:s, where they can influence the world as much as I can, with no specific act structure or story arc.
Some significant part of gaming is risk-free experimentation in a simulated world. The experiments possible are bounded by the simulation quality of the world. More realistic NPC behavior would open up for a lot more games.
There is an older game called STALKER which had (limited) elements of what you describe: autonomous NPCs which influence the game world. Even though it was limited, the NPCs just battled for control of certain territories, I always thought it was a really neat mechanic. It made the world feel more 'real' and alive.
You would see these factions fighting and gaining/losing territory throughout the game. You could chose to help them or just pass on by, but the actions progressed regardless of your choice.
Don't forget there is a certain randomness with 'more natural' and with randomness you're going to invite Murphy to the party.