Because all of the stations are future-proofed for a track configuration where GO has 2 dedicated tracks on the north side and CPKC has 2 dedicated tracks on the south side. See below how the full buildout would look:
Kipling Station (no changes. The corridor is already quad-tracked)
View attachment 540695
Dixie Station (1 new track on the north side)
Cooksville Station (2 new tracks, one on each side)
Erindale Station (1 new track on the north side; new side platform). Or alternatively, 1 new track on the south side
Streetsville station (2 new tracks on the south side)
Meadowvale Station (2 new tracks, one on each side)
Lisgar station (2 new tracks, one on each side)
CPKC Milton Yard (2 additional tracks; no changes to yard access)
View attachment 540696
GO Milton yard (2 additional tracks; no changes to yard access)
Milton station (1 new track on the north side)
If GO uses the northern pair of tracks, the only significant station construction required would be to add pedestrian tunnels/bridges at Dixie, Lisgar and Milton stations. The existing pedestrian bridges/tunnels at Kipling, Cooksville, Erindale, Streetsville and Meadowvale would not need to be modified at all.
I think it's clear from the overhead images that relocating all the platforms, pedestrian bridges/tunnels, and the Milton GO yard to the south side of the corridor and relocating the Milton CP yard to the north side of the corridor would be far more expensive than just adding additional tracks with the existing platform and yard configurations.
Meanwhile at the Humber River, a new bridge is required regardless of whether it is part of a rail-to-rail grade separation.
View attachment 540694
I suspect that sum of the costs to completely rebuild every station, build a new CP yard on the north side and build a new GO yard on the south side would be more than the net cost of building the new Humber River bridge such that the passenger line swaps sides with the GO line.
If it turns out that the sum of all that stuff is still cheaper than the net cost to swap sides at the Humber then yes the right solution is indeed to completely rebuild the entire corridor with platforms on the southern pair of tracks.