LNER claimed tickets from Haymarket are not valid from Waverley.
They are incorrect in claiming so (unless it's an Advance, but we aren't talking about those). The tickets permit Break of Journey and are valid via Waverley, thus you can start/end short there if you so wish.
In any case, how exactly, particularly if you book it as a paper ticket, do they propose knowing whether you actually did start at Haymarket or not? Waverley has multiple separate gatelines.
TBH I've always struggled with how grossly incompetent this aspect of the trial has been. I get that they can't prevent people splitting (the way to prevent that was going to be to have faster Edinburgh trains so create fewer splitting opportunities) and there will always be less obvious workarounds unless and until this becomes a national policy, but it seems bizarre that they didn't do it for all flows related to Edinburgh, Newcastle and Berwick to/from Kings X and Stevenage rather than just those individual specific ones, as sale of Haymarket/Manors tickets will have made a right mess of their statistics and people were always going to work that out quite quickly.