Manufacturers sell to shops at a trade price, let's say 75% of the full retail price. The retailer makes their money from this 25% difference in price. TheyRetailers can reduce the retail price from their cut, if they think that this will attract more customers, in order to sell higher numbers.
The retailer hopes to make more money from a slightly smaller margin by selling more units.
There is no difference in the hardware, and you get the same access to Apple's services - iCloud, Music, TV, etc. You can take it into an Apple Store if you have a problem with it.