On the contrary, I find that seeing myself as only a chemical machine is a very freeing experience that leads to greater happiness and contentment.
I find it strange that you can talk about concepts of 'you' being 'factually' correct or incorrect when there are very few established facts about consciousness or self - it all seems like mostly open philosophical debate from what I've seen.
I don't think you are necessarily in disagreement with him.
The fact we are machines doesn't mean the circuits to video game analogy is incorrect, in fact I think it's apt.
If physics is about understanding the fundamental nature of matter and energy then why do we study chemistry? Because they are different abstractions that yield different insights.
So the point is thinking about consciousness may be more useful that thinking about chemicals even if we understand some of the low level mechanics.
You could try Pillars of Eternity. Also, Fallout 3: New Vegas was done by Obsidian, not Bethesda, and Obsidian has many of the same staff that worked on the original Fallouts 1 and 2.
Pillars of Eternity is really fantastic. I dropped more hours than I'm willing to admit on that game and I might pick it up again when I have some more free time. I'm also really looking forward to playing Tyranny.