Margin is (price − cost) / price. Markup is (price − cost) / cost. They are different denominators. A 50% markup on cost is not a 50% margin on price. The page shows both from the cost and price you enter.
A product that costs $60 and sells for $100 has a $40 profit. Margin is 40%. Markup is 66.7%, because $40 / $60 is two-thirds. Pricing from a desired margin uses price = cost / (1 − margin).
Overhead, shipping, and advertising are in the cost only if you included them in the cost you typed. Tax on the profit is not removed.