There are two interlinked issues on ShipStation. The first is that the customs invoice isn't showing the prices in the local currency to the customer (i.e. the currency they paid in). The second is that there's no way to automatically determine if an order is within the IOSS threshold (150 EUR).
It is always recommended to provide the customs invoices in the currency the customer has paid in. This is to speed up customs clearance, but also gives more reliability in terms of how much the customer will pay at the border. This is even more important with the EU's IOSS scene where there's a 150 EUR threshold.
For example, consider the following scenario. You sell a product at 149 EUR on your website from the UK, and charge German VAT at 19% (so the customer pays 149+28.31 = 177.31 EUR). Because the intrinsic value is under 150 EUR I can use my IOSS number on this order. The problems are 1. I have no way in ShipStation to automatically add my IOSS number to these orders (there's no price-without-tax and there's no currency conversion), and 2. since the customs documents are in GBP (not EUR) if the exchange rate changes between the time of order and the time when the order arrives at EU customs there is a risk of my parcel being above the threshold, which means the customer will be double-charged VAT.
Do the customs invoices in the local currency, where possible.
Make is possible to automate the process of adding the IOSS number to an order.