Are you seeing anything beyond those which I'm missing? If not, then I'm not oversimplifying it
What you are missing is that the second one is part of the first one, killing a NPC can be a way to progress a quest, can you really not picture any reason to kill somebody beyond a random act of violence? Describing as nonsensical havoc the full effect that a dead can have is oversimplifying the possible consequences of it
..and these are all factors that another game with day & night schedules had to deal with (Skyrim). However, Bethesda prevented many problems by not allowing players to kill critical NPCs
Please tell me that this is an aprils fools' joke, none of those factors have any meaningful impact in that game, in fact, I think that you can become the mega ultra archmage knowing only like 3 novice spells. Morrowind? I'll give you that, but Skyrim? That has to be one of the worst examples of player agency I can think of. If that's your frame of reference, I can see why you find pointless one of the options the player has, hell, I'm surprised that you don't find every option pointless based on skyrim.
You should really try the Ultima series, but if you have, and you can't see a difference between the ocean of possibilities in one and the binary (and that's being generous, unary is more fitting) approach of the other, I honestly don't know what to tell you.
Also Bethesda games are buggy as hell, is an awful counterexample in every possible way
