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More than likely the email is being rejected as you state because the SPF record for the sending domain either doesn't exist or doesn't match the From field.
Not quite sure how to solve it given MVE breaks orders up by vendor and then sends them on behalf of the vendor You should be able to force your default_company_orders_department value as the From field which should then match up with your SPF. I would probably use hooks rather than modifying a distributed file so your changes aren't overwritten at the next upgrade.
Note that many spam filters don't like "relay type" email. I.e. someone sending on behalf of another.