That could happen, in theory, though I find that highly unlikely. This deal with almost certainly have the approval of the area Councillor and that usually settles things.
That said, as theoretical matter, yes, the City could over-ride a positive planning report. Generally that would lead to an OLT appeal and the City would almost certainly lose when going against its own planners.
(they would have to hire outside planners to argue that City staff got it wrong).
The only challenge for a developer in that context is time, given that towers are rising now.
However, they would likely get an expedited hearing, and they would likely win.
The accretive cost to build the additional floors is quite low when the land is already bought and paid for; the drawings and approvals done; and the building already rising and you're adding standard floor plates. This is 'give-me' money.