We have been experiencing this same issue since we moved onto shopify in 2018. To date there has been no resolution and we’ve only been told that “a feature request has been entered with the development team”. That was in December of 2020. We’ve received no follow up from the development team since that reply.
We’ve managed to make due with the issue up until Shopify’s recent release where they are now displaying discounts on a line item level in shopify admin. This display is broken and not showing the correct amounts that were actually applied to the order (you can confirm this by viewing a customer’s order confirmation page vs the same order in shopify admin). This display change has greatly exacerbated the issue and is causing extreme pain for our customer service team and their ability to tell the customer what they paid per line item.
We, along with many other merchants, need a fix for this.