When a store owns its own inventory it is natural to tailor recommendations to optimise margin gain - its largely testament to the technological illiteracy of brick and mortar stores that margin is rarely factored into personalised web positions such as search results. It is very much factored in when designing store layouts, catalogues, and ad campaigns.

In all these other places there is a contention between getting the customer exactly what they might want (discovery) and getting the customer to buy what you want. Note that stores want the customer to buy items that will most cost them (overstock) as well as items that will most profit them.

This way the store manages this contention becomes a key part of its public image / brand, and affects its long term perception and customer base.

How this heavy push from personalised recommendations to personalised advertising will affect amazon is going to be interesting.