Oswald would have had to zero in his rifle as he brought it in in pieces.
The scope should hold the "zero" it had, provided it wasn't detached from the barrel assembly. If Oswald used the scope and was familiar with any deviation from the rifle's "zero" (due to changing distances, etc.), he could compensate.
May be why the first shot--accounting to some theories--missed. Then, if he reused the scope, he had a better sense of the compensation. Or he decided to use the iron sights. Either way, a first shot that happened to miss did him some good in the long run.
The main thing about zeroing a rifle is to make sure it doesn't fire left or right of the intended target. The shooter has to compensate up and down with his (or her) aiming to allow for shooting at a target that might be close or far away. This is why lho prob used the iron sights. He had no way to know if the rifle would fire left or right of where he positioned the crosshairs of the scope as he obviously could not zero in the rifle once inside the TSBD.
You're comparing the shots taken from the SN with competitive precision firing at a shooting range or the Olympics. What Oswald did--if he used the scope--was a field improvisation; he took his chances, made corrections and got lucky on the head shot, which was a near-miss.