It's giving the passenger the choice of which it's going to be: full single fares or prosecution.
Yes, as I understand it, it's either, or.
Charging the undiscounted anytime single fare to a specific station is only mentioned in condition 9.2 as one way of dealing with a passenger, on a train, who cannot produce a valid ticket. Another is reporting them for prosecution. They should not be charged the fare for a new ticket AND reported for prosecution.
Isn't it the train company, rather than the passenger, who gets to choose?
Once a train company has decided not to charge a fare for a new ticket on the train, but to report the matter for prosecution, that fare ceases to have any relevance. The company simply chose not to charge it, so it can't be considered a loss the company has suffered due to the actions of the passenger. Therefore it shouldn't be the basis of a settlement.