I cannot see any reason for that. The Routeing Guide lists GN + BS as valid routes. GN is the map for Newcastle - Glasgow via Carlisle, and BS is the map for the WCML (& connecting routes) from Scotland to the West Midlands.
So, by the routeing guide, follow map GN from Newcastle to Carlisle, and map BS from Carlisle to Birmingham (via Preston)
It doesn't cause an anomaly, as a CAR-BHM SVR is cheaper than a NCL-BHM SVR.
Finally, if you ask East Coast's website to buy a SVR (Off Peak Return) from Newcastle to Birmingham, travelling via Carlisle, it will happily sell you a ticket at the same price as the direct journey.
I do think some ticket clerks misunderstand the rules, in particular, although a direct service, or a shorter route may exist (and is automatically permitted), that they are not the only permitted routes, although they may be the most commonly used ones, and believe the rules to be that if a direct or shorter service exists, you must use it.
To be quite honest, it cannot be beyond the wit of ATOC to write a database which will list out the permitted routes for a ticket, which can be given as part of a ticket purchase upon request. I'm not saying they should always do this, but in all honesty, it is part of the contract formed between the passenger and the TOCs, and in the long term it is in the best interest of all parties to have their contracts self-explanatory.