There is a CRM system setting 'Order Confirmation Email' which allows you to specify a document that is sent when a quote is put into one of two states, "Customer Acceptance" or "In ERP system".
The CRM also has an internal order notification email that has a toggle as to whether to send only for CMS order confirmations, or all order confirmations.
As there is no functionality to specify a document template in the CMS Order Confirmation plug-in, it would be good to have a toggle for the 'Order Confirmation Email' setting to apply either only for CRM, only for CMS, or for ALL orders.