To add fee on checkout for auction winner you can use code snippet below in your functions.php file. To change percentage of fee just modify global_fee or fee_per_auction variable.
add_action( 'woocommerce_cart_calculate_fees', 'afw_add_fee_on_checkout' );	
function afw_add_fee_on_checkout( $cart_object ) {
    $global_fee = 0.00; 		// initialize special global fee, value 25.45 means fee of $25.45
    $fee_per_auction = 0.30; 	// fee per product, 0.25 => 25%
    foreach ( $cart_object->cart_contents as $key => $value ) {
        $product_id_cart = $value['product_id']; //get the product id from cart
        $quantity = $value['quantity']; //get quantity from cart
        $product = wc_get_product( $product_id_cart  ); //
        if('auction' == $product->get_type()) :
        	if ($product->get_auction_closed() == 2){
				// fee for auction with highest bid
				$item_price = $value['data']->get_auction_current_bid(); // get winning bid price	
				$global_fee = $global_fee + $item_price * $quantity * $fee_per_auction;
            } else {
				// fee for buy now auction
				$item_price = $value['data']->get_price(); // get buy now price	
				$global_fee = $global_fee + $item_price * $quantity * $fee_per_auction;
			}		
				
       	endif;  
	}
    if( $global_fee > 0 ) {
		
    	WC()->cart->add_fee( 'Buyers Premium', $global_fee, true, 'standard' );
    }
}Fee for autocharge orders:
add_filter( 'auctions_for_woocommerce_stripe_automatic_charge', 'auctions_for_woocommerce_stripe_automatic_charge_addfee', 10, 2 );
function auctions_for_woocommerce_stripe_automatic_charge_addfee( $order, $auctions_id ) {
	$fee_per_auction = 0.10; // 10% fee
	$product      = wc_get_product( $auctions_id );
	$item_price   = $product->get_auction_current_bid();
	$global_fee   = $item_price * $fee_per_auction;
	$item_fee     = new WC_Order_Item_Fee();
	$item_fee->set_name( 'Buyers Premium' );
	$item_fee->set_amount( $global_fee );
	$item_fee->set_total( $global_fee );
	$order->add_item( $item_fee );
	return $order;
}