Very few people do long journeys such as Dundee, or even Edinburgh, to Newquay by rail. It's similar on the Mrches Line, though there are some people like myself who will travel from south west Wales to Manchester, most of the other passengers are using the services for journeys like Carmarthen to Swansea, Cardiff to Newport, Cwmbran, Abergavenny or Hereford, Ludlow to Crewe, and so on.
I don't think that TOC's are very bothered about knowing where their passengers have come from. They will be more concerned with revenue. Long distance through services are not being run for the benefit of long distance passengers, they are run to get the best use out of the stock by cutting out turn around times as much as possible while offering a service pattern that tries to help maximise revenue from all different types of passengers, regardless of their starting and finishing points.