You have quite the active imagination. The term I have consistently used is "mainline". Is every train in your world a freight? And have you ever considered the basis of many waivers, namely temporal separation? Freights occasionally use the Bala south of the by-pass too. And if that track is electrified (likely only to the Don Spur and up to Midtown) then the freight will have to comply with Metrolinx terms, not the other way around.Yet you and others keep saying that they will run on the same tracks as CN freight trains. That simply will not happen.
Meantime there's lots of options for paralleling the CN Bala up to RH, and then running the service into the Relief Line tunnel, ostensibly at Don Mills.