Tunnelling must cost more than that because you are estimating between $125-175 million a km, while in reality it is closer to $300 million a km.
Tunnelling is just a tunnel with a concrete shell. It does not include rails, power, radio, wiring, safety equipment, emergency exits, drainage pumps, lighting, worker walkways, emergency exit shafts, or trains. Sometimes, like Eglinton, it didn't even include the TBM launch and extraction holes which were tendered separately.
Also, that $50M/km does not include soil testing, engineering, or community consulations around where it should go or in many cases the extraction pits for the TBMs. It also doesn't include TTC staff overheads (accounting, money management, project management, ...)
The TTC's $300M/km (or $400M/km) quotes are for a completed product from start to finish, including rolling stock, storage yards, maintenance equipment, testing, inspections, internal staff costs, etc.
There is a lot that goes into the holes once you remove the dirt and put in the shell.
Station quotes are closer to a finished product (escalators/elevators installed, and finishes) but will not include track level equipment.
Worth noting is that station quotes also include some track spaces like room for power equipment and switches/turnback/train storage areas.