Would you believe it? Two rail companies seemingly arguing between themselves leaving the poor passenger caught in the middle of the contradictory information they're giving out? Sounds like there are faults on both sides - Merseyrail might not like it, but Northern's actions can be binding on them (as some Penalty Fares exclusions depend on the situation at the start of the journey), while Merseyrail is probably right to highlight some of the implementation flaws in Northern's Promise to Pay invention which it seems to be in no hurry to fix. A better answer might have drawn its conclusions by reference to how the company interprets the penalty fares regulations.