Why do discounts not apply when manually creating an order in the Shopify backend using Custom Pricing?
Custom Pricing is designed to automatically apply discounts using draft orders the moment a customer takes a product to checkout. Manual draft order creation does not trigger this discount application, as the product has not gone through the checkout process. To see the discount applied, the order must be created through a checkout process initiated by a customer.
More details on this can be found here - https://support.boldcommerce.com/hc/en-us/articles/360040469492-Custom-Pricing-General-FAQs.