Flexi does not include any special function for matching payments from payment gateways that charge a transaction fee. In general, the amount of the paying document must be the same (or greater) to fully settle an invoice. An internal document cannot be matched with any document or payment.
From Flexi's perspective, one possible approach would be, for example, to record a receipt of CZK 100 and an expense of CZK 3 instead of a receipt of CZK 97. The invoice for CZK 100 could then be properly matched with the payment, and the remaining CZK 3, as an expense, would be posted as needed.