I do not think it likely that e.g. grocery stores are expending capital to develop and implement systems to give there customers leverage to pay them less money, with no benefit (never mind net benefit) to the grocery store.
It's more likely that there is a side to the art of tracking that you do not account for, than the idea that the grocery stores are so benevolent.
I think the idea is that if one in a loyalty program, and it provides them with some discount/benefits, then they are more likely to shop there instead of at some other chain. This way they spend their money at that chain, and that is good for the store. It's just one more way stores are competing with each other. It also provides the chain with some data, but I am uncertain of its utility. I don't really believe it to be useful for them in general for anything other than targeting.
The benefit to the store is that they can more closely monitor consumption patterns across time (e.g. people buying X will also frequently buy Y, but not necessarily on the same grocery trip). I don’t see how this is harmful to the consumer.
It's more likely that there is a side to the art of tracking that you do not account for, than the idea that the grocery stores are so benevolent.