This is exactly what happened. The choice was done in spite of the history of the design of the system as it operates today, and forces the creation of a separate network that is completely and totally incompatible with the existing system.
And the problem is that doing so will not allow them to take into account any of the efficiencies possible of a bigger system. Rather than just a yard to wash the trains and perform light maintenance, they need a facility that has the ability to lift heavy components out of the cars, and even the cars themselves. Because they are using a different line voltage, they can't tap into the TTC's existing 600V DC system and have to build an entirely new system from scratch. If there are any delays with the rolling stock deliveries, or defects that result in all of the trains being pulled out of service, there is no potential to borrow rolling stock from the other divisions.
Had they built this line out on the suburbs were it didn't have the potential to connect with the existing system (or have very limited connections), then I wouldn't have an issue with choosing a different design. But the Ontario Line goes right through downtown, and interfaces with elements of the existing systems at almost every block. It's silly and wasteful, and is so representative of the harmful "We know better than you" mindset that permeates through Metrolinx.
Dan