Yes, when you start an Exchange, you can add additional items to the basket including Products.
So if you want to take additional fees as part of the Exchange, you can set up an Exchange Fee as a Product, add them to the basket as part of the Exchange transaction and charge the customer.
You can also set up a Visibility Rule on the Product whereby it only appears for a return transaction, i.e. when you're exchanging Tickets in the Box Office page.