What about the difference between the “negatives” (with the optical effects applied to them) and the OCN (the reel that was in the camera back then)?
Even if they conformed the official “negative” into something else, there should remain the OCN frames somewhere for all scenes with optical effects (wipes and optical compositions etc).
With the OCN frames all optical effects would have to be recreated digitally which is probably a lot of work.
The wipes were actually redone optically (using the actual camera negatives for the relevant shots like you mention) as part of the restoration process before they made any changes. I think this resulted in the wipes not beginning and ending at the exact same frames and technically still counts as an alteration from the original version, although maybe someone can clarify if I’m wrong about that.
The vfx shots were re-composited digitally, presumably using the original VistaVision negatives (again, someone can clarify if I’m wrong). This definitely counts as a change, not only because the recomps were done digitally (although recomping of any kind would still be an alteration), but also because it resulted in slightly different positions for all the various elements.