Two Scenarios for One Order Confirmation Email

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I have a store that sells standard products on the store, but also custom products that are manually entered as a Draft then converted to an Order. We need to include a note about the custom product itself in the email confirmation to the client. Right now, internally, these notes are getting saved in Notes but ideally this would get captured in the confirmation email with {{note}}. Using the Shopify notifications feature, I originally thought we'd have to use a Draft email for custom orders and save the Order Confirmation email for 'standard' purchases but now I wonder how I could code this into the overall order email - has anyone done this before who could help with the right way to approach this?