If the total amount of the letter of credit includes commission, it will generally be deducted directly from the value of the goods. How to pay the commission should be done according to the agreement between the buyer and the seller, and you can't guess at will or ask for other people's opinions.
There are generally two forms of commission in international trade. One is commission, which can be deducted by the buyer before payment. One is the secret commission, which is usually required by the middleman. The seller must remit the full amount to the middleman after receiving it.