An invoice managed by Auto Invoice shows the tax selector again, so you can apply a custom percentage, Tax Exempt, a tax preset, or a supported Auto Tax rate. A tax you set stays yours through later order, shipment, customer, exemption, and invoice address changes, and an ordinary save no longer rewrites a tax you did not touch.
You can also add, edit, delete, and reorder your own discount lines and extra shipping fees, in one section at the bottom of the invoice. Managed order lines, shipment-linked fees, packing, and Auto Pack stay locked, and manual discounts and fees that were hidden behind that lock are visible again.