Are you saying that Warrington to Manchester via Newton-le-Willows is NOT valid with a Widnes-Disley ticket?
To be a valid route under the current routeing guide, it would have to be:
a) the shortest route (it isn't - that's via Glazebrook);
b) using a train which calls at Widnes and Disley (there are none); or
c) on a mapped route between an appropriate routeing point associated with Widnes and one associated with Disley (they all go via Glazebrook).
Warrington-Stockport (and Warrington-Disley) is a little different, as you can start from Warrington Bank Quay, and the shortest distance by train to Stockport or Disley is via Newton-le-Willows and Manchester Piccadilly.
The rules don't specify that this refers to routes exclusively by train, but this is an assumption you often see here.
That's what the published routeing guide says.
Until the end of last year, the routeing guide (which determines where a ticket can be used) had a rule in it which said that journeys no more than 3 miles longer than the shortest route are also valid.
This rule (or something based on it) is probably what led the TPE site to give the itineraries JakeF found. If you can find something similar today which allows you to catch trains into Victoria around the times you would need them, you should have no problem if anyone does question your ticket.
While this is a case of journey planners using different rules to the published ones, it doesn't mean that either set of rules is necessarily bad, or that you can't rely on either when it suits you.