In that case you will have to do the currency adjustments yourself.
If you input the purchase invoice into QuickFile in Euros then you could set an exchange rate on that and this would then be the rate used to calculate the GBP values for your VAT return. When you make payment you would log it as a cross currency payment specifying the number of pounds you sent and the number of Euros the supplier received, and QuickFile would automatically record the difference in GBP values as an entry on the currency charges nominal (credit, in this case, since you paid out less than the GBP value of the invoice).
If you’re recording things in GBP then you’d have to do the same by hand. Represent the currency exchange service by a dummy bank account, then tag the money you send to them as a bank transfer to that account, and log the purchase as paid in full from the same account. This will leave a balance on the account (either positive or negative) representing the currency fluctuation, manually create an appropriate in or out transaction to bring it back to zero and tag that to currency charges via “something not on the list”.