The admin commission for each sales should be calculated as
(Total Item Price + Total shipping & handling fees) x % of admin commission
Total Item Price x % of admin commission.
As sellers can set the product price as free and charge everything as the shipping cost. Which means the admin gets nothing. This is a BIG loophole!! Even Ebay will use final value which is (item price + postage and handling charges) to calculate the fees that they charge for each sale.
You have to assign users shipping cost and other extra costs into a variable. You need to create a couple of function for getting the shipping cost and extra cost for that particular seller. Then assign the variable into this array value – 'net_amount' => ($order->order_total * $percentage)/100. Which will help you to meet the requirements.
If you can not create a function or accomplish the flow of logic then I will request you to please hire a developer. A developer knows how to implement a logic.