Shipping costs defined in "Shipping costs management" is not applied to orders. To me there are two known problems:

Prices in the shipping cost matrix is never used because there is a problem injecting the correct shop_id in the ShippingCostCalculator service. PR for that problem is available here
New PR here : here
 
Second problem, is that even though the ShopPriceProvider adds a price line for the shipping, this is never shown to the end-user on checkout.. Only after confirming the order will he notice that the price has increased according to the defined shipping costs

So let me be explicitly clear : When shipping costs are configured, the customer will be billed higher than the amount he actually confirms....