It is redoing. The effects weren't complete until the compositing was done; this was its own art, and until it was finished it was just a bunch of bluescreen elements. The composite is the effect. It was a hard job, and took many second, third, and fourth attempts. You had to film the bluescreen elements with the composite in mind. You had to take the time to make a proper matte--there was dedicated matte artists to just do the extractions, which is why some matte lines are better done than others. When you combined them, you had to make sure all the elements were aligned right in the composite, or else it would be all out of place. You had to make sure the opacity was correct, and you had to compromise where it was necessary. You had to print them with certain colours, because they never printed correctly--in fact, sometimes bluescreen elements would be painted "wrong" in order to come out "right" in the composite. You had to take into account the film stock, in order to get the right amount of contrast, knowing it would change, and you had to chose a specific format to account for generational degradation, which added its own aesthetic. They knew they would be compositing things on an optical printer, and it informed the very approach they took.
Once you start re-compositing things, you aren't dealing with the original visual effect. You are dealing with the original elements only. And once you start tossing aside the original effect and going back to the individual layers, you might as well start adding and deleting some--which is why in pretty much every edit where they have done digital re-comps, they have added in new elements as well.
I'll say it again: the original visual effect wasn't complete until it was composited. It wasn't some incidental thing, a final element to the effect that can just be polished up in the digital realm. It was the effect. If you want to have any pretense about "Restoration" or "Preservation" you have to present these as they were. Getting rid of the original composites is removing all the hard work those artists strove to do, to make seem believable and pleasant looking on the screen. And sometimes, it wasn't a total success--and that's an important facet to preserve. The struggle, the flaws, the failures--as well as the slight-of-hand, the successes, and the invisible work that they sometimes did.