Creating an underground rail system will be messy. There will be a significant amount of digging from the surface, despite the tunnel being bored. The Contractor has tried to choose routes which will minimize the inconvenience, but there will be disruptions.
For example, I have been a promoter of putting the west end of the tunnel under Slater instead of Albert. The contractor supports an Albert tunnel in the west. If we look at the disruption involved in each option, the Albert option can avoid some disruptions.
In the above graphic, the contractor's Albert line avoids the LeBreton development lands and is low enough to lanch the TBM before the bend of Albert. The blue line is a trench which doesn't need to be covered for most of its length.
The red line is the straight line to Slater. However, it involves a new structure for Albert. (Probably about $20M.) This would be disruptive because Albert would need to be temporarily detoured. Also, during the construction of this section, building on the development lands would be limited. Future buildings would need to straddle the tunnel, but that should not be too much of an issue for a new building design. Another issue might be that the green triangle between Albert and Slater is under NCC control. The red line would also be a trench, but might need to be covered in some areas.
So there have been a number of things which have been taken into account which are not necessarily as obvious as they could be. I think that there could be interim reports which detail a lot of the thought which has gone into the current offering.