Anybody is free to go to court if they feel they have been incorrectly treated.
Parliment decided over 150 years ago that failure to pay for a rail journey is a criminal offence and can be prosecuted through the courts. This has been refined and reviewed by parliment regularly, these laws are not Victorian relics.
A lot of people on here get confused between a "Customer Service" matter and a "Breach of bylaws" matter, and seem to think that Passenger Focus can have some impact on criminal law, as opposed to customer complaints.
As has been said before on this thread, no passenger can be forced to accept a Penalty Fare or out of court settlement. They can always proceed to court if they feel their mitigation is that good. Most do not, one would assume on legal advice of some sort.
The TOC's are obliged to protect their revenue, and if anybody is unhappy at the powers Parliment have given them, then get on to your MP about it, that's who changes the law.
But while drafting the indignant letter demanding the money-grabbing TOC's get their come-uppance, come up with some solutions for protecting revenue as well, as what most people who do not work in the industry will not recognise, is that there are a significant number of people (of all classes, social backgrounds and ethnic groups) who will not buy a ticket without fear of consequences if they don't.
I see them day in day out. Very very few of them (I can count on one hand after eight years the one's I have personally been involved with) end up in court.