1) Because then Rob Ford may actually support it. Would you rather spend the extra $30-50 million, or save $4.6 billion by having the whole project scrapped? Your choice.
2) Because a subway running 3-car trainsets, ATO, and running at high frequencies should not grind to a halt because a car decided to run the light and gets T-boned by a train. Especially when that accident occurs at the only intersection on the entire line.
3) This really isn't that big of a deal. The cost of the Eglinton line has nearly doubled since it was first proposed. Why aren't you crying foul about that? When you've already tacked on an extra $1 billion to the intial pricetag, what's another $50 million to make sure that it's operationally independent, and will actually get built? To me, an extra $50 million on a $4.6 billion project is a ROUNDING ERROR. In fact, when you look at that $4.6 billion figure, the extra $50 million doesn't even cause that $4.6 to round up to $4.7.