The inventory for the items in the builder will be decremented after the customer checks out, once the payment has been processed.
The inventory should always update, no matter what your settings are. If you use the 'Use your own products' setting, then it adds the SKUs to the order, so the inventory updates naturally. If you don't use that setting, then the app will automatically go into the included products and make the amendment.
If your products are not decrementing, ensure that you have your products set up to enable inventory tracking. Read this Shopify help article to learn how.