Well, for fun I thought I'd see how much the tunnel could be raised if the three downtown stations were moved a bit to the west. Here is the result, shown in light blue:
The station which moves the most is the Downtown-East Station, followed by the Rideau Station. I could have moved the the Downtown-East Station to the east, but it would have then been farther from Bank, which I think is an important pedestrian street. Also, the Rideau Station can't be moved east because of the curve so moving Rideau west consolidates the gap between stations to the length between Rideau and Campus Stations. (I am not sure why they drew the Rideau Station smaller than the other underground stations - I corrected that.)
Personally, I would still put the Downtown-West Station diagonally under the new Central Library and come straight along Slater from LeBreton instead of doing the curves under Old Wellington at high speed.
So, in general, it should be possible to raise the tunnel and stations by about ten metres just be moving the station locations. A side benefit is that the Rideau Station moves farther west so there could be justification to add another station at Laurier (under Waller).