It says that "we would strongly advise you to make use of the journey planner". After the events of the last year I am sure we are all familiar with the difference between strong advice and law!
If you can't get your chosen route to show in NRE or another journey planner then of course it will probably be an uphill battle with staff on the frontline (and even then, not all would accept NRE itineraries as valid).
But if/when it comes to discussing things afterwards, a journey planner is not an absolute necessity to prove a disputed route. It certainly helps, but I wouldn't suggest that a ticket can't be used over a permitted route just because journey planners won't offer an itinerary.
It states that NRE reflects the Routeing Guide, but we know that is not always the case. In any case, the disputed routings section doesn't deal with disputes over what the permitted routes are.
It gives the procedure for situations where it is agreed that something isn't a permitted route, but where it is argued that it would historically have been a reasonable route (and should thus be restored as a permitted route).
I quite agree; using routes that aren't 'obviously reasonable' will often be a risky strategy. It has to be considered whether there are alternative means of using the ticket (or alternative tickets) that have less potential for conflict.
That's true, but you need to know what journey planners to use and how to make the most of their "features"