This harks back to the debate had many times over, and quite significantly a few years ago (2011) where it depends on the actual stations noted on the ticket. For example if the ticket said from Pontefract Stations to Leeds then my interpretation - supported by the response from ATOC at the time - said that you were not free to choose which ever of the Pontefract Stations you liked to take a longer journey, but had to choose the relevant Pontefract Station to start from. The example given at the time - very similar to this example - was Bradford to New Pudsey (i.e. you decided to start at Forster Square and go via Shipley and Leeds and not start directly at Forster Square) was declared as invalid by ATOC. At the time Journey planners offered it as a valid journey, but negative easements were added as the journey planner software obviously wasn't interpreting things correctly! Other examples were Farnborough Stations to Blackwater - i.e. is it valid from Farnborough Main via Basingtoke and Reading? The answer again was no, you had to choose to travel from the relevant Farnborough station, in this case North.
So, in summary, my view is that a Pontefract to Leeds ticket is not intended and should not be valid via Church Fenton, but the journey planners are offering it in error. As a matter aside there are quite a few similar errors creeping again of late, especially in the North West where there are all sorts of dubious double backs and protracted journeys being offered as valid when they shouldn't - and in some cases haven't been offered previously.
The routeing guide maps behind NRES seem to lurch from one set of errors to another!
If you had a valid itinerary printed out, however, then I expect it to be honoured.