True. I think it should happen in close together phases if possible.Hopefully NPR will be built in full, but I suspect that there will be several intermediate stages. For example, before HS1 and HS2 phase 2b was/is built, Eurostar and HS2 services appear on the existing main lines, until the new lines are operational. NPR might be the same, with Trans Pennine Route upgrade filling that void.
Phase 1: Manchester Airport to Leeds (enabling HS2 connection)
Phase 2: Leeds to York (or Church Fenton)
Phase 3: Liverpool to Manchester Airport (with line also towards Crewe from Liverpool via Warrington)
The issue with suggesting things like Liverpool - Chat Moss - NPR through Pennines - York - Newcastle is that extra infrastructure has to be built for that connection onto the main line. Ideally HS2 and NPR would have its own underground station, meaning no reverse for NPR and less land clearance above ground.
Looking at it now, maybe keep faster Liverpool to North East services on using TP route but have through HS2 to Leeds via NPR services. Once all of it has been built, then change services over.