Okay, Mary MacDonald at Heritage Preservation has gotten back to me, and here is the answer that none of us will be very happy to read:
I have double-checked everything. When the designation was done for the property (1976), explicit reference was made that the Simpson's Tower was not included. The original listing (1973) was for the older portions only as well. Given that in 1973 the Simpson's Tower was only 4 years old (7 in 1976) it is understandable that there wasn't enough perspective on the modernist movement to inform an understanding of value. Of course, the designation could have been amended to include it after time had passed, but the necessity to do so wasn't on anyone's radar.
All Hudson's Bay needed was a building permit. They applied for one and got one. No other planning process was necessary. I cannot speak to the matter of the design review panel, though it would be atypical for a building permit application to be reviewed, and no link with the planning division to facilitate.