I figured that the force-field helmet things must have been filtering out the yellow sun, so that they got a dose of it once their helmet was broken or turned off. The atmospheric differences was an interesting addition, but that wouldn't have been the whole story. I think it would have made more sense if they also had red lighting on the ship that matched Krypton's sun. Lois and Ghost Jor-El changed the atmosphere in the ship; they could have changed the lighting at the same time.
Earlier in the thread there was a debate about how kryptonite could be reasonably incorporated into this version of the story. Both Kal-El's ship and Zod's ship used the Phantom Zone projector to basically go through hyperspace to get to Earth. The exploded fragments of Krypton would have taken the long way through normal space. Maybe it's taken this long for any of the debris to reach Earth, and some of it will start falling as meteorites in the next few years?
"It is a remarkable dichotomy. In many ways, Clark is the most human of us all. Then...he shoots fire from the skies, and it is difficult not to think of him as a god. And how fortunate we all are that it does not occur to him." -Batman (in Superman/Batman #3 by Jeph Loeb)
