Why are the discount code boxes not displaying on the checkout page for products with Custom Pricing discounts?
Custom Pricing version 2 and 3 use the Shopify draft order checkout. By default, discount codes can't be applied at checkout on draft orders. However, Custom Pricing version 3 offers Discount Code Stacking which allows your customers to enter and use specific types of discount codes on the cart page. You can read more about this feature here: https://support.boldcommerce.com/hc/en-us/articles/24362120759700-Discount-Code-Stacking