For the SE, they went back to the camera negatives, the raw footage, to recomposite most (but not all) of the shots. I’m not sure to what extent they did this with the composited effects shots (which were all done in VistaVision so the final composite would not have increased film grain over non-effects shots) or whether they kept the original composited elements.
They did this extensively, at least in the first film. The whole reason for the garbage mattes disappearing isn’t because they tweaked the black levels, it’s because they re-composited the foreground elements against the background elements. In all space shots you will notice the positions of the elements are slightly different. I’m under the impression that all re-composites it were done digitally rather than optically, but whatever they did they did it to every shot with compositing in SW as far as I can tell anyway.