This feels like the proverbial dollar left on the street that economists say should not exist, so I'm racking my brain trying to figure out what's stopping chains from replicating this. I wonder whether this alternate network is as scrupulous about source tracking and food safety regulations. Those costs could be driving up prices on the traditional retail side.
Scale.
Anything living has a level of variability and likelihood of failure/damage/spoilage to it that gets harder and harder to manage as your scale gets bigger.
When you're a small shopkeeper who sells about 3 baskets of apples a day, it's both easier to sift through it and throw out the bad ones AND easier to find 3 basket's worth of apples that meet your quality expectations.
When you have to move 3 pallet-loads of apples, though, not only does QC become a more complicated endeavor, but you have to find 3 pallet-loads of apples to sell at a competitive price, so you may not have the luxury of being so choosy. When pallet-loads scale up to shipping-containers. . . you can see where I'm going with this.
And then there are logistics issues. If you're a large retailer you have to bring everything into centralized warehouses and then send them out. This means things need to travel longer distances and/or have longer shelf-lives. The upshot of that is they have a higher chance of either being past their prime by the time they get to you, or that had to get picked before they were properly ripened on the vine.
When you're smaller, have smaller scale suppliers, and less complicated distribution networks a lot of that extra burden falls away. Starbucks had this problem when they first started to get big too. A lot of people give them flack for over-roasting their beans and giving everything a charred/muddied flavor. When they were small they were able to be choosier about the beans. As they grew the scuttlebutt is that there just weren’t enough beans of that quality level on the market, so they had to lower the quality threshold and move to darker roasts. They still sell better beans, but only in select locations.