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

<?php

namespace Customize\Service\PurchaseFlow;

...

class PurchaseFlow extends \Eccube\Service\PurchaseFlow\PurchaseFlow
{
    /**
     * @param ItemHolderInterface $itemHolder
     */
    protected function calculateTotal(ItemHolderInterface $itemHolder)
    {
dump($itemHolder);    // ★呼ばれない
        ...
    }
}

services:
  eccube.purchase.flow.shopping:
    class: Customize\Service\PurchaseFlow\PurchaseFlow