It will probably be slower due to running underwater by then.
Hopefully the next generation of trains will have some kind of submarine capability.
This scheme although not the best possible solution for any proper gains in travel times in the South West is probably the best that can be done at the moment with regards to the money available and keeping the route open that serves the current towns.
As has been pointed out by others the sea defences will need to be maintained anyway, and this effectively boots the problem a few decades down the line for the next generation to worry about.
If sea and water table levels continue to rise and that rise also starts to speed up, then much of the GWR route from the Somerset Levels right down to Newton Abbot will be under threat.
As will many of our coastal communities...