Great question, and I’d like to be able to do this too.
My first thought was to see if order.totalDiscountsSet.shopMoney.amount > order.cartDiscountAmountSet.shopMoney.amount, since only order.totalDiscountsSet.shopMoney.amount contains line item script discounts. However, it seems we can’t compare multiple variables in Flows at this time, we can only compare a variable with a static number.
So I’ll go back to the drawing board and maybe have to do this with a private app/webhook or possibly an Arigato Automation.
It would be really nice if Shopify provided a data source for which Script Editor scripts made edits to an order so those could be more easily tracked for reporting and finances.