This is anecdotal, so take it with a grain: I worked for a credit card processor about a decade ago, and it was routine to have the merchant run a penny transaction on the terminal, and refund it post testing to make sure it works.
They're fairly large processing over $40b in annual transaction volumes, and there wasn't any stress about not doing it again post testing (the only stress was the customer wanting a refund for the transaction costs).
If it is a merchant bank, or network requirement, it's either explicitly for card not present transactions, or not well followed. The important factor was handling of the credit card information (PCI DSS compliance).
