Every pair of stations has a separate set of permitted routes; they aren't calculated recursively (I.e. just because Wigan to Huddersfield is valid via Manchester, that doesn't mean that it inherits all of the valid routes between Manchester and Huddersfield). Such a system would arguably make sense but it isn't how things work.
It's also worth noting that aside from anything else, for Wigan to Leeds, it may well be that the Calder Valley is within 3 miles of the shortest route - whereas for Wigan to Huddersfield, it's comparatively more of a detour (you go east of Huddersfield before heading back west) and I would be surprised if it's within 3 miles. Routes within 3 miles are permitted even in the absence of "mapped" routes.
Easements are unlikely to have any relevance here; it's just a question of an oversight when setting the mapped routes across the Pennines. It certainly isn't the first example and it's unlikely to be the last.
Having read a number of threads about these rules on here and being familiar with Northern services from Wigan to Yorkshire having used them almost exclusively to reach Yorkshire destinations, is it not the “direct train” rule, rather than the “3 mile” rule that takes precedence?
Monday - Saturday, Wigan Wallgate - Leeds services are routed via Atherton, the Calder Valley and the various West Yorkshire stations between Brighouse and Leeds, with journeys from Wigan, Hindley, Atherton etc all being valid this way due to the direct train rule. Connections at Hebden Bridge for Halifax, Bradford Interchange etc aren’t a problem as the Calder Valley remains the shortest route, but otherwise this would not be permitted due to the Huddersfield route being shorter and the fact that as you mention, permitted routes are not recursive, despite it being illogical for the journey suggested.
Traditional railway geography also plays a part, with Wigan’s location on the Lancashire and Yorkshire Main Line still bleeding through into current service patterns, often making the Calder Valley the faster option from Wigan and points west to Southport and Headbolt Lane. I recall attempting to buy a ticket from Southport to Batley which would have made use of the direct service from Wigan Wallgate to Batley, but as it is not direct from Southport, no itineraries were available. Trainsplit showed the only option being tickets split at Littleborough, with potential journeys via Huddersfield taking over an hour longer and requiring long waits at both Manchester Victoria and Huddersfield, compared to only a few minutes at Salford Crescent for the Calder Valley option.
I have also travelled to Halifax via Huddersfield and Brighouse, but never attempted to reach Huddersfield from Brighouse. Before this system of “any permitted route” was introduced, did passengers ever encounter such problems?
