Right, which is why they can go ahead and trip it when you root, but there should be a way to completely factory reset, including resetting Knox. That said, we manage to make credit card payments online via rooted devices all the time, so I'm not sure the idea holds water that payments via a rooted device are completely impossible. (Still, I can certainly see that it might not be worth their time. The factory reset shouldn't be very difficult though.)
Apple their bricking last week and this is very much because of the liability shift October last year. If manufacturers cannot show their equipment is safe the merchant pays for the fraud which means merchants will not accept those means of payment as a result.