"not the Invoice, therefore it will only take the formatting from the Sales Order template."
You can make Many of these templates; you then get to assign which is the "Packing Slip" and which is the "Pick List."
"The line which reads "Sales Tax xx%" prints on our packing slips"
Lists menu > Templates. Edit that Template you are using. Go to Additional Customization, the Footer Tab. Remove the checkmark in the Print Column for the Sales Tax entry. Now you still see it on the screen, but it no longer Prints.
"and it should not. It is creating confusion to our customers. Again, this is due to the template driver coming from the Sales Order Module that you referenced in your picture, rather than the invoice module."
You control Everything you are asking about.
Please see my attachment.