That's the whole issue.
Imagine all the vehicles turning from Yonge southbound wanting to go eastbound on Lake Shore, then vehicles turning northbound and eastbound with the new Yonge/Harbour intersection. Then you'll have vehicles turning southbound on Yonge trying to get Downes St (Harbour St extension).
Then add all the buses trying to turn from Harbour northbound to Yonge, then turn again westbound on Lake Shore.
All with the city's inability to properly time signalized intersections.
It's all a recipe for a complete disaster, and a gridlocked congested mess. The ramp reconfiguration project idea needs to die, it's not a good plan at all.