Access a community of over 900,000 Shopify Merchants and Partners and engage in meaningful conversations with your peers.
https://shopify.dev/docs/admin-api/graphql/reference/customers/customerpaymentmethodsendupdateemail On this mutation, it says you can pass in email variables to override the subject, body, or add a custom message.
I attempted to do that but it still just keeps me the default Shopify email, none of my customizations are on it.
This template only supports a subset of the EmailInput parameters. It can only use the from and bcc parameters. I have created an internal ticket to update the documentation and discuss allowing more customizations to this template.
Sorry for the confusion.