WooCommerce API: Create order with meta data on line item
You can't specify the product variation data when placing a order, the product variation should already exist and shall be referred to using the variation ID.
For example if you would place a order of the "black" variation (say it has variation ID 12):
"line_items": [ { "product_id": 1, "variation_id": 12, "quantity": 1 }]
Adding metadata to a product variation can not be done using the orders
endpoint, use the products
endpoint for updating products.