It is different. In the checkout case, the cashier's intervening negligent act led to you getting the item for free.
It might still be theft (or fraud or some related charge), but only if those laws create a strict liability crime out of keeping something that you know was given to you by mistake. I'm not sure but I think there might be specific laws to that effect if you knowingly take advantage of a bank's mistake. Whether there's a similar law in general, probably depends on where you live.
In the pure theft case, there's no intervening act by a store employee. It requires criminal intent.
The argument that if the customer knew, it's theft, applies equally to cases where the product is rung up incorrectly, which several other people in this thread have claimed to have witnessed. I guess we're all thieves now. I've been overcharged and undercharged at stores.
Also even if the intervening act by the store employee doesn't matter, it would be impossible to prosecute. They'd have to show that the customer knew the checkout person missed the item. How would they do that? Interrogating people you live with to find out if you mentioned it to them? No, they don't have access to admissions on HN years later.