Sorry, was going off of the prices you misquoted. Still, the point remains that the price delta is retail price delta. That's the only factual data we have. We have no idea what apple actually pays for the drives themselves, but given they charge full price difference between 128 GB and 256 GB models, I see no reason to believe they are taking losses or even poor margins.
Tear down sites have noted that the increase from 16GB to 32GB or 32GB to 64GB NAND for iDevices is usually only about half of the $100 increase they are charged for.