Thank you for choosing the Community to assist you with your concern about updating the email message in your invoice templates. I'm here to share some insight about this feature.
Currently, saving a different message per invoice template is unavailable. To send a personalized message to your customer, you need to enter the specific verbiage in the Message to customer field.
I can see how important it is to have this option in your account. Rest assured, I'll take note of your suggestion to see if this feature will be available for future updates. All enhancements to QuickBooks functionalities are largely the results of feedback provided by users, such as yourself.