Just as TOCs▸ aren't happy with split ticketing on rail services. Fortunately though, passengers have the protection of the National Rail Conditions of Carriage and, despite ATOC» moaning about split-ticketing, they have no real appetite for the political and public relations fallout should they try to amend or remove Condition 19.
I'm pretty sure the changes of last summer did away with the anomaly, but I think bus fares from Bath to Corsham used to be more expensive than Bath to Chippenham via Corsham - a slowish journey that competes with the train. There was absolute horror, and "you CANNOT do that", when I suggested at a bus user group meeting that people buy a Chippenham ticket and get off short. And rail rules for advance tickets (and megatrain) also outlaw the practise, with potentially expensive penalties and occasionally not just potential.
It feels wrong to be charged more for the shorter journey, and it feels wrong not to be allowed to get off short in cases where that rule applies. The only case I personally can see where shorter-costs-more would feel right is if the short stop station / stop was more expensive per passenger to operate.