Oh! And by the way, I think you will find that the local fares are set by SYPTE and WY PTE rather than Northern.
I cannot comment on SYPTE, but in the case of WYPTE this is no longer the case.
I had a discussion with a contact at WYPTE last year as regards the horrendous anamolies on local fares in West Yorkshire. My contact at Metro advised me that whilst WYPTE sets the prices for all the assorted Metrocard and Day Rover products, as well as the concessionary flat fare, the basic rail fares are set by Northern. And whilst WYPTE may be able to offer influence and set general fares policy, they do not actually set the fares themselves.
One of the problems that has sprung up over the years with the different operators fare policies is that many have not considered the routing implications. For example, Halifax to Manchester is Rte Any Permitted. The fare is set by Northern, and as per the routeing guide is valid via Huddersfield. Yet it is cheaper than the Huddersfield to Manchester fares set by TPE. The reason, I suspect is that Northern have considered the fare in relation to the other fares to and from Manchester from calder valley line stations - as before the Brighouse link reopened this would be the only way. Then the Brighouse link reopened and that way became valid to get to Manchester, but the fare was never adjusted accordingly - even though in BR days the fare from Huddersfield was higher than the Halifax fare to begin with. This is what has led to the many anomolies that we now find.
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Some fares setting issues are caused by route restrictions being removed. Not that long ago there used to be two sets of fares for Leeds to York. 1 set, the cheaper, was Rte Direct, the other more expensive was Rte Harrogate. The Burley Park to York fare was unrouted, but was the same as the more expensive rte Harrogate from Leeds. Thus if you went via Harrogate you paid the same as if you went from Leeds, If you went via Leeds you paid the same as going via Harrogate, but more than passengers starting the journey at Leeds - which seemed fairly fair.
Then the Rte Harrogate fare was removed, and over time the Leeds to York fare set by TPE is now more than the Burley park to york fare set by Northern. Yet the Burley Park fare is now valid via Leeds. So, in this case keeping the Rte restriction in place would have been fairer all round. From Burley Park you could offer a cheaper fare via harrogate if you wished, while retaining the higher fare for going via Leeds.