Yes, it does sound like the person didn't give you the right discount, unless perhaps try don't offer a "whole bag" discount, which I think would be strange.
That being said I don't think it's at all fair to assume you'll get the same discount as ordering online, especially via Amazon. In many cases the online side of the business is a completely different entity. Ordering online means drop shipping from a warehouse somewhere with very different shipping rates and very little overhead costs. To have 55 bags of grain delivered to a LHBS retail shop is likely more expensive (Amazon shipping discounts wouldn't apply) and there's much more overhead that needs to be accounted for in the product markup. To sell it to you in person at the Amazon rate would likely be selling it at a loss for them and not a sustainable business practice.
I see what you are saying but I just cannot see how shipping 1 bag is less expensive than shipping 50 bags or 500 bags. The higher the volume, the lower the cost. That's the law of business.
Otherwise, can't the brewshop get their own amazon prime account and ship from their own warehouse to their own shop and make money?