If you want to process invoices with order reference from edoc invoice fully automatically, you must have enabled the vendor invoice workflow in Microsoft Dynamics 365 for Finance and Operations.
When you use the edoc D365 FO invoice cockpit option Include invoices into the automation process for vendor invoices, the invoices are processed according to your configuration of the vendor invoice workflow.
Here's how
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In the navigation bar, click on edoc invoice cockpit > Setup > Bases > Parameters > Invoice.
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In the Invoice with order reference - Settings section, select the option Include invoices into the automation process for vendor invoices.
All incoming invoices with order reference are now processed fully automatically by Dynamics 365 for Finance and Operations. The extent of the processing depends on your configuration of the vendor invoice workflow.