Going back to the original query: Are you allowed to make a non-compulsory walking interchange in order to arrive at the shortest route(e.g. Warrington Central to Warrington Bank Quay)?
I agree with RJ that the shortest route cannot be be calculated using a walking interchange. This would lead to absurdities such as unaccompanied minors and people with mobility problems being compelled by NRE to undertake, sometimes significant, walks, perhaps at times of day when they'd rather not do this.
As an example, the shortest route by rail between Blackwater and Fleet is via Ash, Aldershot and Brookwood. I doubt if anyone would want to do this as the journey time is in the region of 1h45m for a point to point distance of 6 miles.
NRE reports that walking changes between either Farnborough and Farnborough Main or North Camp and Ash Vale are permitted. The rail element of each route is shorter than the shortest route and, given the abysmal bus connections between Blackwater and Fleet, these routes make sense for those who don't mind a walk.
The only ticket routeing is VIA FARNBORO NTH, which covers all 3 options.