Last I heard, the big chains like Safeway have found no external monetizing use for this linkage and have given up on trying to do anything with it. "Some people seem to buy stuff" is as far as it gets. The cards have turned into an IQ test: if you use the card, you get competitive prices; if you don't, you're a dope and you pay higher prices. Some people refuse to use the cards; all the better for Safeway.
It's similar to the shenanigans played with Coke vs Pepsi. When one is on sale, the other isn't. If you follow the trends, you can always buy the brand that you want when it's "on sale" -- if you don't, you're statistically paying a higher price over time.
/jordan