The profit margins are not large. However they do not have to be. Retailers aren't so much buying the products as they are renting out their retail space to manufacturers. For every game or console they sell. They take a percentage of the sale. They take no real risk beyond shrinkage. Which is entirely within the retailers control. This is the reason for glass casing the merchandise.
Basically its a safe sales practice. The retailer cannot take a loss unless they decide to take a loss, or do not protect their inventory properly. This is why retailers are able to sell games and consoles in the first place. When they do not sell the manufacturer reduces the price or the unsold merchandise is returned. That leaves it up to the retailer to control distribution and floor sales as expenses.
The reality is that the retailer does have to meet a quota of sales to cover these expenses labor, insurance, transportation, location upkeep. That said they do generate profit from the allocated space which is minimal in locations. Since all they allocate to the sales is usually a single aisle, and that aisle brings in customers that make additional purchases.
The reason smaller retailers work the trade in system is that the profit margins aren't high enough for them. Not only because the margins are relatively small, but because it is hard to move games in the kind of bulk required. Your local game boutique will generate a profit from the sales, but not necessarily offset their expenses. For instance if you generate a thousand dollars of profit in a day. Then have to pay employees wages, insurance, rental fees, and corporate kick back. Well that is a small margin of error to live within. Basically a bigger retailer actually has lower costs compared to the smaller player.
I don't necessarily blame these little retailers for their trade in policy. Any more then I blame car dealerships for their trade in policies. The reality is that this is one of the advantages of being a small retailer. They have the ability to enact such systems, because they can afford to be more hands on. While the system would be impractical for a large retailer.