no I agree the film itself restored was combined with the special edition shots… But that does not mean the fx shots were designed against the print itself. As the restored print was probably was not available to design the fx shots to match to.
It seems to match the laserdiscs more so or broadcast telecines in my opinion and that colorspace.
This explains the discrepency i feel.
I have a couple of references of the 1997 SE print, and I don’t see the discrepancies you are referring to. The digital shots were inserted into the restored negative, after which the restoration was color-timing was accomplished by YCM Labs, which included the new digital shots, I would think.