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 Have you checked expiry dates? Some places buy items that are about to expire (like in a month) at a discount. 
And takes the risk of selling them quickly. 

Maybe thats whats happening here? 
 Ooooh yeah, we need to calculate the price-per-cream-cheese-ounce-day. How many days to expiry do you get per ounce at each store? 
 Believe me, that is an actual thing. 
 No, I think what’s happening is the larger chain with better prices is more efficiently run and can better negotiate with suppliers than the independent franchises. It could also be the difference between unionized and non-unionized workers. I really don’t know. 
 They can also negotiate for cheaper power bills, taxes, and often are able to purchase the real estate they're using.