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Currently backorders are limited to the in stock/inventory status of the product page. Once a customer adds to cart there are no further indicators that an item is on backorder. Not in the cart, checkout or order confirmation emails. Also in the Shopify admin there is no indicator to staff than order is on backorder or which line items are affected.
Just did the same for client last month. Here is how we did that
1. Detect backorderState using javascript , if (cartQty > inventoryQty) then save backorder: true as line item property.
2. Modify cart.liquid / cart-items.liquid to display the backorder warning which is saved as block in settings_schema.json
3. create a custom conditional block in order-confirmation.liquid with the same logic
But we omitted the part where the order is flagged as backorder using orders/create webhook
what we implemented was mostly theme dependent and focused on enhancing the user experience layer.