Scripts and Workflow bypassed on automatic purchase orders

We have the special and drop ship order feature enabled and are automatically creating purchase orders from sales orders selecting the "special order" dropdown in the create po column.
I have a script that updates a few fields on those purchase orders and can confirm that the script did not trigger on beforeSubmit, but it did update in the afterSubmit. That is fine however, we also have a workflow for po approvals. It appears it is bypassing this workflow (it has before record submit trigger type) as I cannot see anything in the active workflows or workflow history of the PO.