From the Guide-
“If you are purchasing multiple inventory items, you don’t have to manually calculate cost as per each inventory item. If you have freight-in cost to be proportionally allocated across all purchased inventory items, select Inventory on hand account, then select Freight-in item.”
This is fine when items and freight are on one purchase invoice but when there is two invoices, one for items and one for freight you can’t.
Think you have to allocate freight proportionally to each item on freight invoice.
I think you are correct and not missing anything @hendra98h