<?php
// namespace Eccube\Service;
namespace Customize\Service;
...
class OrderPdfService extends TcpdfFpdi
{
    ...
    protected function renderOrderDetailData(Shipping $Shipping)
    {
        ...
        foreach ($Shipping->getOrderItems() as $OrderItem) {
            ...
            // 税込金額（単価）
            // $arrOrder[$i][2] = $this->eccubeExtension->getPriceFilter($OrderItem->getPrice());
　　　　　　$arrOrder[$i][2] = $this->eccubeExtension->getPriceFilter($OrderItem->getPriceIncTax());
            ...
        }
        ...
    }
    ...
}

services:
  Customize\Service\OrderPdfService:
    public: false
    autowire: true
    decorates: Eccube\Service\OrderPdfService

<?php
// namespace Eccube\Controller\Admin\Order;
namespace Customize\Controller\Admin\Order;
...
// use Eccube\Service\OrderPdfService;
use Customize\Service\OrderPdfService;
...