It would make sense for recomposites to have a different balance between the inner core and the outer glow, since they're two separate pieces of film. As we can see with the lightsabers, no effort was made to match the new digital composites to the old optical composites.
The desaturated lasers...could that be a recomp mistake of only comping in the B&W "core" animation element and not the separate colored glow element? Looking at the '04 Star Destroyer flyover, the lasers not only don't have any color, they don't glow period. They're just white lines. I don't think they're just desaturated, I think someone fell asleep at the switch and forgot the glow layer entirely.
7 years later, I'm still dumbfounded at the lack of quality control.