He was completely contained in that environment though. In BvS he's still out in the open in our planet's conditions. Snyder himself has said he hates kryptonite so it wouldn't surprise me at all if he changed what "kryptonite" is and how it effects him.
Another thing to look at is Zod. Zod adapted himself to our conditions and had no trouble going back and forth between them.
Hmm, I guess the painful reaction only happens once when a powered kryptonian naive to exposure is placed in that atmosphere. Supes definitely had a rough time when he was initially depowered. You're right though that with this being out in the open and with how quickly he recovered once his space dad reverted the atmosphere in his cell, this is probably something that works much differently.