You seem to be riding an incredibly weird hobby-horse into the discussion. I can't imagine that as many as 1% of the passengers on London-Edinburgh trains across the year are travelling on international passes. Furthermore, as a company which appears to be almost unreasonably revenue-focused, I strongly doublt that LNER is doing anything to encourage or benefit these passengers.
It's likely only to appear 'weird' if the default expectation is that the numbers involved are as small as some may suppose.
However, the absolute reality is that a two-day First Class BritRail all-UK Flexi Pass, valid on any services network wide, including peak, currently costs cGBP213.51 at spot exchange rates.
This information is widely available to and discussed by potential international inbound travellers, not just in the English language, and compares to a domestic customer wishing to travel between London and Edinburgh return with LNER being offered the same flexibility for up to GBP654.60 when no Railcard is held or valid.
Random observation during ticket checks, especially on well-loaded services ex-Edinburgh, would suggest that inbound travellers are
very aware of the opportunity that these passes present, and use them extensively.
The actual percentage of passengers using them will, likely and rightly come under 'commercially sensitive' provisions, of course, but London to Edinburgh - the primary focus of this timetable revision - would appear to be one of the most popular flows for this particular type of ticket.
Amongst the varied range of impacts and effects that the new timetable may present, then, effectively providing more capacity for low-yield custom between two discretionary travel honeypots
should be taken into account, when other cohorts are subject to disbenefit.
It becomes even more relevant when the industry messaging is in part about modal shift between from air to rail, for which there's little to no evidence, but one of the impacts of pursuing that strategy is, potentially, to actually encourage modal shift from rail to road within regions negatively affected by the changes.
The point is that passholders are such a minor part of the numbers that they haven't been a motivating factor in developing the timetable, as you hint. So yes technically they're low yield but they're something you just have to accept.
Actually, that's not the hint.
The hint is that those designing the timetable may not be taking this cohort into account much or at all, because either the data on them is poor, or because no-one is incentivised to take them into account, or both.
Lest there be any misunderstanding, the suggestion is not that this should be a 'major' consideration on its own, any more than students compelled to reach Newcastle College by 9am should define the timetable, but they both exist and it's relevant to consider all stakeholders.