I don't think it's clear that one is not permitted to break their journey when travelling on a direct train from origin to destination that does not follow a shortest/mapped route.
The guidance on how to use the Routeing Guide (
here) is a bit self-contradictory in this regard.
The second paragraph says: that "a through train is advertised in the National Rail Timetable as a direct service which offers travel between a customer’s origin and destination stations as provided on the ticket that they hold for the journey being made. This route may not be a permitted route if a change of train is necessary to complete the journey."
This meaning of this appears to be that the route is permitted as long as the train could, in principle, be used to travel directly - that is, as long as nothing
requires passenger to change. This implies that whether or not they actually travel directly in practice does not affect the validity - as long as every train they use calls (or has called) at the origin on their ticket and subsequently calls (or will call) at the destination on their ticket, they are fine.
However, the flow chart underneath says, about cases where one is "travelling on an advertised through train", that "the route is a permitted route for that journey", while in other cases it is just stated as a "permitted route" without the "for that journey" bit. This suggests that the through train rule only applies if the passenger is actually making the whole journey on the through train, and defaults to not being permitted (unless something else makes it valid) in all other cases.
I have no idea what, in reality, the rules are in this area. Perhaps someone who is better informed than me could comment?