By selecting the Margin option you are saying you want to use cost plus whatever percentage you choose. Unless MAP is higher the app will default to the margin you set.
f you are looking at the Shopify products page displaying margin this is a different calculation than ours. Technically we calculate Markup (not margin). We calculate the margin before applying currency. The warehouse cost + 40% (or example) + item estimation for shipping is equal to the displayed price of the product.
Here is an article that explains the difference between margin and markup.