The byelaw offence is parking
on any part of the railway where charges are made for parking by an Operator or an authorised person without paying the appropriate charge at the appropriate time in accordance with instructions given by an Operator or an authorised person at that place
. Authorised person includes 'an employee or agent of an Operator' and 'any other person authorised by an Operator'.
Railway has a pretty broad meaning. It is defined to mean railway asset which includes a station. The act they lifted that definition from defines station to include a car park. I have never been able to pin down exactly how far from the actual station proper you can get before it becomes just a car park, and it probably involves some other issues that I would be happy to go in to if you want.
You could argue that if you pay the amount on the majority of signs you have paid ' in accordance with instructions' but if there is a sign at the only place to pay instructing you to pay £3 you probably have to pay £3. You might be able to argue that as violating byelaw 14 is a criminal offence the court should interpret any ambigious area in the wording in your favour, but I don't think it's ambigious enough for that to work.
As to whether it is ethical to increase the charge a company makes for parking in its car park, I don't see any problem, especially as I paid £3.80 this morning for an offroad car park. 'Draconian' means imposing a death sentence for minor crimes and has grown to mean imposing a very severe penalty for a crime, not a large price rise.