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.
If 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.
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