@ForTheLoveOf. Your arguments have become very difficult to follow and almost circular, so I can only refer you to my earlier posts regarding the applicability of 9.4.
As it happens, I don't think it right that a customer is forced to pay extra to mitigate a delay caused by earlier disruption to their journey on the supposed National Rail network. There should be a provision in the Ts&Cs to avoid that, but as far as I can see, looking at the applicable restrictions, terms and conditions, there isn't. I respect the fact that you disagree.
The customer didn't need to wait 4 hours. Their ticket was valid on the 15:02 departure from St Pancras, using EMT and XC to arrive at Newcastle at 19:33, which is still a significant delay versus the intended arrival time, but is an option which nobody here has mentioned. Was it mentioned to the customer at the time, as an alternative to either paying the excess or waiting for the 19:00 departure from Kings Cross?
The OP is rather sparse on detail, probably quite properly, for reasons of confidentiality. But I would be very interested to know if the validity of the the tickets offered for the customer's itinerary was fully explained by the retailer and in particular what the customer's options would be should disruption mean the requested itinerary could not be completed. If the retailer sold the tickets on the basis that in combination they would be valid for travel on the 15:00 from Kings Cross, that would put a very different complexion on the matter.