> I thought they just returned unsold boxes back to the vendor?

Even in the cases where the vendor/distributor allowed that (and discount bins were a thing because they often did not, at least at no restocking fee), the retailer still accepted the risk that the vendor or distributor would be defunct. If they had a consignment model where they only paid contingent on a retail sale, that was different, but (at least AFAIK) that was never the norm for boxed software.

The discount bins you mention illustrate the previous poster's point: That developers used to get far less before the App Store existed.

If Electronics Boutique can dump a $50.00 game in a discount bin for $3.00, how much do you think it paid for that game in the first place? And how much of that amount went to the author?

The amount they spent in the first place is irrelevant, that's the sunk cost fallacy. They sell it for three dollars because that's their best expected return (weighing in factors like opportunity cost of keeping the box on the shelf).