Re: Kryptonian Physiology in Man of Steel
The powers are related to the sun. The differents atmospheres are just "parasites" that neutralize the capability to use them, but they're still there.
Superman on the Black Zero, still has his powers, but he is poisoned, so his weakness keeps him from using them. When Jor-El turns the atmosphere to ours on the ship, Superman is healed and can finally use his reserve.
At this point, Zod and the others kryptonians are powerless because they're not in a direct contact to the sun, probably because the ship is protected of the radiations.
When Zod arrives on Earth, and this time in a direct contact with the sun, he gains powers but like Superman before, he needs his atmosphere to fully use these powers. At the end of his fight at Smallville, without his helmet, he's still powerfull but poisoned and forced to leave.
Both atmospheres are just an acclimatization question, nothing to do with being powered or not. I think.