My suggestion is to add a either another set of choices to the Price Export box or add a checkbox called something like "Use Discounted Line Item Price" which would export the line items with their price after discount.

The purpose behind this is to solve the issue where shipstation is also connecting to a shipping company which is creating export documents, the line items need to be priced correctly since each line could have a different tariff.

The current module can bring in discounts as a separate line item which would work if everything has the same harmonization code.

I have already solved my situation by using a preference in a new Magento Module to override the entire Export class which now the Base Price - Discount. The down side to my solution is if/when shipstation updates their module, I will have to remember to compare and modify my code at the same time.