In fairness unless the industry moved away from 'market based' to 'kilometric' pricing then there will always be discrepancies where splitting tickets will save money - some bigger than others.
There would still be issues surrounding 'kilometric' based prices too as many journeys can be via different routes of varying length.
Anything else is just tinkering around the edges. Plus at the moment, where one split is etadicated another could be created.
A split model (as has happened recently with mobile phone contracts) might work.
I.e. a kilometric distance fee, plus a kilometric operator fee, (plus a HS1 premium if applicable

) equals a consistent ticket price. Journeys on the WCML would be more transparently competitive between VT/LM!
It would have to have route-restriction regulations that don't currently exist, paired with diversionary acceptance agreements during disruption.
Where it would shine is on multi-segment journeys, where your base distance fee is flat across the changes, but operator fees step up and down automatically.
It could even be smart enough to price the distance portion variably if your journey crosses a peak boundary -- although that could also be implemented with the current fare model.
For journeys with multiple interchangable routes (e.g. East Croydon - London Terminals // Liverpool Lime Street - Manchester Airport), a compromise distance could be arbitrarily set in the database.