I don't see that building a spur to MCC would impact Cooksville (or any of the stations further east). I can't see re-routing the entire line as an option. The only thing I've ever seen GO publish on the subject, did have the service to MCC passing through Cooksville - but how they'd achieve that I don't know, unless the entire thing was in a tunnel with a portal east of Cooksville. Though it's not even on the more recent long list of projects.
If you were to get GO to MCC (be it a spur, or continuing along the 403 west to the existing line), I'd think you'd follow the alignment of the TTC's 2001 proposed Line 2 extension from Kipling to MCC, diverging grom the existing GO track half-way between Cawthra and Hurontario, with a new station near Central Parkway.
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