Hello there, Blackburns.
I have a workaround so you can enter a different message for each estimate.
Currently, there's a change in modifying an estimate. The message defaults to all estimate forms.
As a workaround, you can use the Add footer text field.
Before saving, give it a name that will differentiate it from the other estimate.
Also, when you're ready to create an invoice from the estimate, you can check this reference: Create and send estimates in QuickBooks Online.
I'm just a post-away if you have concerns about converting an estimate into an invoice. I'll be happy to lend a hand.