Its kind of gotten complicated due to the absorption of Smarttrack into GO RER.
It all depends how "Smarttrack" is implemented from a fare perspective.
They will all use the same trains, however, if "Smarttrack" means a free ride for TTC passengers, then it might only be offered on the originally planned "Smarttrack corridor" (Mount Dennis to Unilever). Or, Metrolinx might just say #&$* it, anywhere in the Toronto downtown borders on the GO-RER system is TTC fare.
I doubt the latter however. I doubt Metrolinx will even offer TTC fares for any part of their lines at all really. Maybe an extra $2 or something if you are transferring to/from TTC, but for nothing? Ill believe it when I see it.
So for now, Smattrack is just an ideology that has been carried over to other GO lines downtown as well. Until fare integration is figured out, the rest is up in the air.
This is what happens when you incorporate two plans together. It becomes a homogeneous confusing political bubble.