Here's a thought for a temp workaround. Make the Shopify message simply read as an ackowledgement, such as:
Thank you for shopping with us today. Your order # is XYZ. You will receive a separate order confirmation separately.
You'd put the acknowledgement phrasing into the subject.
standoutd I think what you mentioned is the approach that many using 3rd part apps use but the main complaint here is that customers should not have to revieve 2 emails confirming their order.