Because they claim they added the edits directly to the original source master they created.
It wasn't a master they cut up, it was the original negative.
They did it, at least in part, for good reason: it had to be treated and cleaned. And as different parts of the film were shot on different film stocks, each one had to be given a different treatment.
More troubling to the restoration effort was the fact that all the effects shots had degraded to the point of being useless.
When copying photographically every generation away from the negative you go brings a reduction in resolution and an increased amount of grain. With some of the effects shots going through the printer several time it soon begins to add up. This is especially problematic when cutting between something shot in the studio and a multi element optical. You go from a relatively sharp, fine grained image to a soft grainy one. It is jarring to see.
To mitigate this ILM used larger negative area VistaVision cameras (larger negative = more resolution + smaller grain = more genrations of printing before the image becomes unacceptably soft and grainy) and printed on reversal stock so they could lose a generation of printing and with it a generation of image degradation.
This reversal stock was cut straight into the negative, and unfortunately was even less archive safe than the rest of the film. Whereas the camera negative was bad but salvageable the effects shots were a total loss.
All the effects shots (those which weren't completely redone) had to be recreated from the original camera elements, and re-composited. This was done digitally and the results were cut in to the negative.
The negative as it exists today is the Special Edition.
The original shots which weren't restored would have to be recreated from the original camera elements or taken from a lesser source such as an inter-positive or inter-negative, should any in good enough condition exist.
It would be a lot of work, and most people would thing entirely worthwhile. However most people's opinions are worth nothing when it comes to this issue. Only one man's opinion counts, and he doesn't want to do it.