I've seen it overridden twice, where the supervisor of the ticket agents sells the second train's fare at the cost originally paid. It seemed to be up to their discretion and required a supervisor to be present and make the decision. I was standing at the next window but have never had it applied myself. Both seemed to be cases that required some sort of compassion (...so not at NYP).

Agreed that the policy needs to change, or there needs to be better coordination between ticketing and connecting services (NJT, WMATA, etc.). Relying on the hope of a supervisor override wouldn't won't work during off-hours or in smaller locations.