There won't be a difference. It will be the same service, all the trains will be GO RER trains operated by GO Transit. Smarrtrack is just a mandate for stations, service levels and fare structure in the Toronto city proper.
If you tap on with PRESTO onto a GO-RER train, at say, Liberty Village station, and get off at St.Clair station, you tap off and you are charged the fare that was determined by Smarrtrack and city council. "Hopefully" a transferable fare that is equal in price to TTC.
If you were to take the same train from Liberty Village and stay on it to Bramalea station, which is in Peel Region, and tap off there, you would be charged a GO transit fare based upon the fare zone structure they implement. Most likely a fare that is similar to GO transit today.