The issue with this is that a ticket from A to D might be cheaper than B to C or even A to C. How can a system be designed to cope with that?
One example is Havant to Ryde Hovercrft port.
If you have a rail discount card then Havant to Ryde Hovercraft Port cheaper than Portsmouth to Ryde Hovercraft Port because within Portsmouth they are not allowed to sell hovercraft tickets and the Hovercraft alone doesn't offer rail card discounts. So what you do is buy it online, whilst stood in one of the Portsmouth Stations and collect from one of the Portsmouth stations ticket vending machines.
There are A to D examples that are solely on trains too.
There is no way you can eliminate that. People who claim it's easy don't understand how fares work.
In the specific example quoted there are various ways it could be eliminated.
a) Railcard discounts could be removed from fares which included the hovercraft.
b) Through tickets via the hovercraft could be withdrawn.
c) Portsmouth could be allowed to sell hovercraft tickets
d) Hovercraft alone could offer a railcard discount.
Of course a) would not be welcomed by railcard holders, b) would be unwelcome to most people who book through tickets, whilst c) or d) would not be welcomed by Hovertravel.
There is also a very easy (in technical terms) way to eliminate such things on UK rail-only journeys - introduce the sort of pricing structure which is used in various other countries. This would not be easy politically of course, and hence is not going to happen.
I am content that I do understand how fares work and will continue to use that understanding to undercut the fares that UK TOCs would prefer me to pay
.