I have not followed all of the very long thread on Leeds-York fares, so
excuse me if this was said and I missed it.

Some posters have opined that a reason why the Leeds-York CDR is seemingly
relatively high, compared with other local routes, is because the PTEs
subsidise fares in their areas.

This is a common mis-conception, PTEs subsidise fares hardly at all, if at
all, although yes, they do pay towards things like multi mode tickets and
day rovers.

PTEs receive money from central government called the Metropolitan Grant
for use in public transport matters, mainly, if not exclusively rail. It
is used largely to enure certain services run which the PTE wants to be
run, which would otherwise be so loss-making that the TOC would not run
them as part of its franchise agreement. INn recent years the MG has
declined considerably, but the sum allocated still counts as part of the
TOCs overall subsidy, another lunatic case of the money-go-round in
railways - unlike normal subsidy payments which go straight from the DfT
(was SRA) to the TOC, the MG is first paid into the PTEs\ piggy banks,
then straight out to the TOC. The reason for it seems to be so that PTEs
can claim, for political reasons that they are spending money on railways,
when in fact no local tax payers money is being spent thus - the same
kind of logic that permits TOCs to boast they have invested millions in
new stock when they havent spent a bean. In WY, for example, the ex-MG
budget for rail is just 2m, and that covers anything from publicity to
new stations.

PTEs are allowed to subsidise fares up to 25 miles outside their areas, eg
WY could subsidise Leeds-York and Skipton, but do not, because why should
they be seen to be benefitting voters from outside their areas, that would
be politically unacceptable.

The reason why Leeds-York is relatively high, for a northern CDR in pence
per mile is that, I suggest, the fare was set years ago by BR before such
things were restricted by inflation-related constraints and by the
vitriolic headlines any rail fare rises get in the media. Leeds-York is a
prime rout,e well served and in a wealthy area and thus, way back when,
some bright spark decided its fare should be higher than many others
regionally. 

In fact, many fares in the north outside PTEs,mor cross boundary, are
cheaper than those within a PTE, and within PTEs fares in pence per mile
vary widely. When asked why there was not a standard rate, thus abolishing
anomalies and the like, the general answer from the industry is that
no-one has the time to re-cast the fares manual, the allowed percentage
rise is simply bolted on to each fare each year, with some variation
according to the markets..

BTW, these days each fare is set byu the dominant TOC for that route, but
I do not know if Leeds-York is TPE or Northern, it used to be ATN.

So, no PTE subsidies, just good old market forces!!

HTH
AB