The fact that only walmart is doing the $100 gift card proves that wal-mart is taking the hit. Remember its on all blu-ray players not just the PS3. If I remember correctly blu-ray players have at least a $100 profit and more depending on the model. I believe the Sony blu-ray player that retails for $399 costs about $265 for retailers. Retailers make barely anything on the PS3. I believe the store I work for makes about $15 off each PS3 sold. Not sure about the $499 bundle though. They do the gift card deal cause Wal-mart isn't losing $100 off each sale because people are going to use those giftcards which in return will do two things a) they will use the gift card and spend over $100 so the hit will be very small b) Buy products with the gift card that have high margins such as clothing.
I can bet you that sony loses less money selling the $499 bundle compared to the $399. They aren't paying konami $60 a pop for each bundle. Probably half that or even lower.