First, they'll never have any change when they do this hoping to force you to overpay. Second, they can charge you for the ATM trip and the wait time (and then you have $20 bills, so forced to overpay). Third, if the machine "failed to run it", they can charge the card and pocket the cash.
The article was about some just charging whatever they felt like, but in those cases got too greedy. Since many won't notice, it's hard to dispute, and the DA isn't going to charge them, they can keep doing over and over. Especially with foreigner tourists.