The margin discount is calculated with the set margin as a percentage discount. You can find this option in the sales agents module. The margin discount option is visible when activating 'may discount'. See below.
Example calculation
Let's take an example article with a unit price of €16.98. If you apply the margin of 2.6 the amount €16,98 is adjusted to €15,36. The percentage discount in this is rounded up to 9.4. Converted percentage discount from applied margin calculate as follows: new amount (€15.36) divide by old amount (€16.98) *100 = 9.45, rounded 9.4.