There's a difference between penning to write and planning a complete line upgrade. The TOCs have gone to NR wroth a list of improvements that have thrown out a lot of the already planning and now look at improving the line speeds alongside wires up. This isn't a simple job and the reality is that there is a huge load on the planning department and looking at the entire route afresh is going to take time. And have multiple stage discussions how can be funded.
The and and half years isn't much time in planning terms. Not for major works.
Up to about 2007, the SRA used to act as the "customer" for Network Rail's major projects.
They arbitrated the design of things like Rugby and the current Stafford scheme, to deliver the best functionality for the money.
After they were disbanded, those roles migrated either to the DfT Rail group, or to the ORR.
Today, I would expect these people to be specifying and reviewing NR's projects.
The TOCs may have a consultancy role in this as current operators, but certainly won't be able dictate design.
I very much doubt the TOCs (TPE I suppose) are able to force NR to dump its plans.
On the TP North route, the west side has been badly treated over the years, while the east side is in reasonable shape.
The west side still has manual signalling in places, and very low speeds either via Miles Platting or Guide Bridge.
Stalybridge has been upgraded recently but is still by no means "fast", especially towards Victoria.
The east side has modern signalling managed from York and has better junctions and alignments by remodelling the former 4-track layouts.
I don't see how a TOC's opinions can stop a major project in its tracks.
If the DfT or ORR has called a halt, or NR itself has decided to have another think, that's different.
We don't even know what NR planned to do to the route regardless of electrification (ie under the original Northern Hub plans).
All we have to go on are raw figures for train frequency and journey time.