The Conditions state:
The lowest priced Ticket available for immediate travel that would have entitled the passenger to start the journey at Poppleton may well be a ticket from Poppleton, in which case it is correct to calculate the excess from Poppleton.
If any industry systems are incapable of issuing that, and are tied to the original origin/destination, then that is a flaw with those systems. If they cannot be overridden, then the only remaining option would be to allow the customer to make the shorter journey without additional payment (which is arguably the common sense approach).