RE: Line of Sight - Line of Bore Qn.
The angle you are referring to is the difference between the line of sight and the line of the bore. I've had trouble trying to explain this to the old timers who refused to believe that the bullet starts to drop the second it leave the bore. They were convinced that the bullet rises when it leaves the bore. And I told them that is because the bore is slightly pointed up just the way you described.
Now, from what I recall, the rifle scope has mirrors and prisms inside, when you adjust the scope you are actually rotating these mirrors. This is why your reticle is always centered. I believe the mirrors or prisms are held in place by opposing springs allowing for up/down, left/right adjustment. So to answer your question, the angle comes from inside the scope.
If sure if I am wrong, I will get jumped on.