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For orders within Australia, we charge GST tax on all stock items and the freight. The stock items tax category auto fills itself in, getting the correct tax category (as far as I understand) from the customer's details.
However, this doesn't happen for the freight tax. This is as the freight tax category field only auto-fills when the Ship Via field is entered. However for us, deciding which freight carrier the order will travel with is the decision of the warehouse when they do the shipment, not the salesperson when they enter the sales order.
So: Can the Freight Tax Category auto-fill based on something else than the Ship Via field? It would be great if it could pick it up from the customer's details like the stock item lines do.
I think that the Tax Category on the DOCUMENT DETAILS tab of the Sales Orders (SO301000) screen defaults from the Tax Category field in the ITEM DEFAULTS section on the GENERAL SETTINGS tab of the Stock Items (IN202500) screen.
I think that the default Tax ID values on the TAX DETAILS tab of the Sales Orders (SO301000) screen defaults from the applicable taxes from the Tax Zone field on the DELIVERY SETTINGS tab on the Customers (AR303000) screen.
As you pointed out, it appears that the Freight Tax Category field on the TOTALS tab of the Sales Orders (SO301000) screen defaults from the Tax Category field on the DETAILS tab of the Ship Via Codes (CS2075000) screen when you populate the Ship Via field on the SHIPPING SETTINGS tab of the Sales Orders (SO301000) screen.
And, unfortunately, the Freight Tax Category field doesn't appear to be available on the Shipments (SO302000) screen for the warehouse to override it.
I think you'd need to customize to get what you're looking for. You'll need to add a Freight Tax Category field to the Customers (AR303000) screen since it only seems to have a Tax Zone field (no Tax Category field). Then you'd have to customize the Sales Orders (SO301000) screen to default that new Tax Category field from the Customers (AR303000) screen into the Freight Tax Category field on the TOTALS tab of the Sales Orders (SO301000) screen.
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