@Abits. I usually avoid reviews this long but I've appreciated your comments on threads and gave it read.
I'm 95 percent with you. [ let that sink in for a moment please

]
Yes! It's not just a video game, it's an RPG, a choose your own adventure in video form.
Where I deviate comes to your Witcher example (which I've not played). Yes, this level of freedom causes problems but the solution is not to restrict the freedom but to have text that acknowledges that you completed the quests out of order as in "oh, you killed Khaga. I can't condemn you for your actions for I harbored the same desires in my heart. You've done us a great service, please accept this a small token of our thanks".
My point is that sometimes narrative can get in the way of replay value. There are many things that make BG2 the best video game ever -- one of them being the unparalleled replay value. PoE1 had an amazing story. Best story in the history of RPGs, full stop.
But the game had little replay value. Am I going to go back to fight the exact same fight with the spectres so I can claim the keep? Sure, I did it three times -- which is something. But am I going to do what I did with BG2 and try every class and every stronghold? No a chance -- all of those different classes were wasted on me. I got to the end, said "great game" and was done. If Obsidian had sacrificed some story for an open world it might have been another story.
Yes, this sometime requires applying 'patches', incorporating implausible dialogues but that has it's own charm. I prefer old neighborhoods to planned unit developments. In a PUD everything is new and orderly, everything works in a straightforward, asceptic manner -- in an old neighborhood houses have weird extensions, make do roof patches, mismatched fencing and questionable lawn art. But give me pink flamingos to suburban hell.
TL;DR sometimes messier is better. This was always the flaw of J.E. Sawyer * his games always end up sacrificing replay value to the god of narrative.
* which I say with great respect. I love his passion and I agree with him 70 percent. Even on weird things like tatoos and steel bikes -- I ride lugged steel and I vote!