Each email template can only be configured to send for one marketplace. This means additional marketplaces need to add new messages every time that you add a new Amazon marketplace. You can easily copy the messages over to the new marketplace by using the "Copy Existing Message" feature.
From the Custom Messages dashboard, select the orange "+ NEW MESSAGE" button in the top right corner, and select the "Copy Existing Message" option. Once the template is selected, any necessary changes can be made to fit for the new marketplace. Within the "Edit Message" section of the copied message, assign the desired marketplace in the "Marketplace" field.
Next, click "Save & Send Test" or "Continue" then "Done" to apply these changes.