The challenge is that NPR is needed to increase available capacity on the Transpennine routes to improve local services by removing faster long distance services. The transpennine route carries far too much of a mix of traffic and the mix between stoppers and fast services (plus freight) causes bottlenecks. There's already challenges in fitting in new stations in growth areas because the line is too full. TRU will only do so much.
And NPR was not just the NW with an extension tacked onto Yorkshire (despite what Andy Burnham thinks); it includes Leeds-Sheffield improvements, Manchester to Sheffield, Leeds to Bradford etc even ignoring the scope creep in Network North.
Unfortunately what will happen is that Manchester will get some shiny new infrastructure that does nothing for the broader north.
Essentially NPR will end up like HS2; promised much but the first sections only built (the line promised to Standedge tunnels will never happen) benefiting the most prosperous areas in the respective region with the best transport systems.