This is yet another case of the rail industry making things worse in a ham-fisted attempt to "solve" a problem of its own making. Most other railways across the world have a clear and simple system for defining permitted routes, either based on mileage or by listing all the relevant options on the ticket. BR simply worked on the basis of "reasonable routes".
The privatised British industry instead has an arcane set of permitted routes defined in the Routeing Guide - a contractual document so complex, yet ambiguous, that no average passenger could reasonably be expected to understand it. Even industry experts and those who are legally qualified sometimes disagree on the way it should be applied or interpreted.
The obvious solution here would be to make it easy to work out permitted routes by having a "Permitted Routes Calculator" tool available online, where you can see a map listing permitted routes at a glance - or to adopt one of the other approaches I listed above.
But no, when the rail industry was eventually forced to deal with the mess it had created, it instead went for the 'cheap and nasty' solution of removing the phrase "Any Permitted" from some flows (as if to pretend that permitted routes weren't a thing?!), and adding inane "via" points to others, such as Bangor to Chester in this case. Result: big-wigs in the industry could pat themselves on the back for having "simplified ticketing", despite having achieved nothing of the sort.
TfW (the government side) is gradually pushing for more of the long distance TfW bus services to be added into timetables, journey planners etc - with integrated fares/ticketing, so need to consider the wider TfW network, rather than just the rail element.
Bangor-Chester interavailable fares were initially changed from "Any Permitted" to route "." in NFM29 (
Jan 2018), but evidently that was still "too complicated" as this was changed to "via Llandudno Jn" just months later in NFM30 (
May 2018).
ATW were in charge until October 2018, so this change cannot possibly have had anything to do with the inclusion of bus services into the rail data, much as that's a laudable move.
In all of these cases I believe there was no change to permitted routes.
There was no change to the Routeing Guide, but in several cases the changes to fare routes had unintended consequences in excluding routes that would otherwise be permitted under the Routeing Guide. For example, many of TPE's longer distance cross-Pennine flows are now routed "Leeds York", even though avoiding Leeds and/or York is plausible - and indeed fastest (especially during engineering works) - for a number of journeys.