I've just had a look at the site. The first thing I noticed was that there's nothing on the page to say what it's meant to do, and there are no links to a more general page. My impression is that it's trying to work out how far a rail vehicle would travel between two points, ignoring the length of the vehicle and any signalling constraints.
If so, there are a few problems with the data used:
It doesn't treat the two lines at Liverpool Central as being disconnected, although Moorfields is treated correctly (albeit using different terminology to Lime Street).
It doesn't include the stock interchange/holding line in Liverpool.
These two mistakes mean that the distance between a Wirral line station and a Northern line one aren't too far out.
It doesn't treat the diesel and electric sections of Ormskirk and Kirkby as being disconnected. I imagine a train could go through the buffers, but it probably shouldn't.
It doesn't account for the fact that no platform in Wrexham General has access to all lines, so a train going from Chester to Wrexham Central has to reverse at Croes Newydd North Fork and Wrexham Exchange Junction. This could be remedied by making platforms 1 & 2 one location, 3 another and 4 a third.
It treats the Halton curve as being bidirectional.
It includes a long-gone railway between Mickle Trafford and Dee Marsh Junction as a route.
If not, maybe only the last one matters.
