Unfortunately it seems to be quite a common misapprehension among enthusiasts that any train service will necessarily be provided for the benefit of passengers travelling end to end. Of course in many cases such journeys are made but much of the time the termini of train services are all but dictated by operational convenience. Many here will be familiar with my interventions in discussions relating to the Wigan-Southport line: one of my most commonly made points is that the number of passengers actually travelling to/from Southport is relatively small. If it was possible to turn trains round at Burscough Bridge I've no doubt that would happen regularly but as it is all such trains have to go to Southport. This is not driven by passenger demand!
And the linking together of what would ordinarily be separate services can provide a better service for those whose journey is across the join location. Some York-Hull services run through to Scarborough, not because Northern wants to compete with TPE for York-Scarborough passengers but to allow passengers between, say, Hessle and Beverley to avoid changing trains in Hull when linking the services together is operationally convenient.
Of course the main argument for not linking together more services is the performance risk ie a late-running train can affect a wider part of the network when running through over a greater distance. Ultimately, putting aside the latter-day issue of franchise boundaries, it's all a balancing act at the planning stage.
