I’ve managed to solve it by withholding the tax for the amount that is different on each invoice, and modifying the invoice template. Manager still tracks the overall withholding tax receivable amount, but the invoices show the way I need with the proper gst charged on the subtotal, and the amounts owing charged to the customer’s accounts are correct.
You appear to be using a custom theme. When you do that, you are responsible for its performance. You have possibly eliminated the Tax column, definitely removed indication of tax being applied, forced inclusion of the Discount column when no discount has been extended, and—most importably—removed the Balance due.
@Joe91’s suggestion about tax-exclusive designation has nothing to do with those.