The DfT promised, from memory, £2.7 billion for TP route upgrade.
That is being called off in chunks, and the £589m for the current works mentioned is the first phase of that profile.
Undoubtedly NR and DfT will tussle over the costs of later phases of the scheme, but the money is still "there".
The question is whether it will be consumed by necessary track/signalling/realignment works rather than OHLE (or robbed for other NR projects).
I doubt that will be answered quickly, until the current phases are seen to be being delivered efficiently by NR.
The NCE piece is also linked to another one on GW electrification, which says that it cost £5.5 billion, twice the previous figure and far beyond the original budget.
‘Onus on industry’ to prove costly rail electrification mistakes are in the past - New Civil Engineer
There is this morsel on the lessons learned from the GW scheme:
The report adds that the “world-class system approach to electrification” developed by the Great Western team will be used on future projects, including power supply that incorporates substantial redundancy, highly reliable components, and safe isolation for maintenance.
One just hopes that this approach doesn't include the gross over-engineering we saw on the GW project.
On the plus side, the political momentum for a full TP scheme seems unstoppable, but the Treasury will have limits to its generosity.