The plan was going to be changed to build the tunnel all the way to Don Mills, since it was easier to launch the TBM's from there, plus the obvious benefits to the operations of the line. But the local community group loudly complained about losing the stop at Leslie, and it seemed like the Liberals were going to lose the upcoming election, so they had to revert back to the already planned alignment and award the construction contract for the eastern tunnels. Of course, the same community group then later complained about construction activity on the surface at the portal.
Yes, it should have been planned differently from the start, but they didn't.