Rolls eyes... You wouldn't choose to put an entire railway into tunnel, that's just economic waste and lowers the cost benefits.
Which is why the number and length of tunnels in High Speed Rail projects have been increasing year on year?
We now have projects in Japan where the majority of the route is in Tunnel (the Kagoshima branch of the
Kyushu Shinkansen runs 88 of its 127km in tunnel, and the Maglev
Chūō Shinkansen will do something similar).
Tunnels are not "cheap now", they are just as costly as they have always been, similarly putting stations in Stratford style boxes isn't a great idea on cost grounds.
Tunnels are getting cheaper, since these days the cost of making an existing TBM drive longer is marginal - the costs are primary procurement and setup of the machiens and arranging mechanisms for the removal of spoil.
Unless you think you can get under the Pennines without a tunnel of sufficient length to justify a TBM the cost of simply extending the tunnel is marginal.
Although I think the route would be too intensively used having such a long base tunnel would also provide a very low gradient route as there are no obstacles and the tunnel can proceed in a near straight line - good for freight.
38km between Manchester and Brighouse with a difference in height of only 30m, which makes it 0.1% gradient - flat enough to be used as a cycle path.
Its a freight operator's dream.
The cost of surface construction is escalating drastically thanks to increased NIMBY activity, the problems of arranging for mass purchases of property and the endless compensation payment demands.
It appears that tunnels are now not that much more expensive than surface construciton, especially in terrain where NIMBY activity will be strong (there is a national Park in the way).
My point about Piccadilly is that through platforms onwards to Liverpool and Leeds would remove a 10 minute turnaround if you used the terminus platforms.
You can turn a train around in 2 minutes, or even quicker as the LU do if you provide a second staff member to drive the central leg of the journey.