Completely agree. And as much as I see the originally envisaged By-Pass as expounded in the IBI report as being do-able, and ultimately cost neutral by savings from all the other cancelled projects (it's estimated that the cancelled need for the K-W line widening alone balances the cost, I think that's a little manic, but it's in that region), why complicate this by biting off more than is immediately needed? The challenge is in keeping third party (non Crown) property expropriation to an absolute minimum, and the simpler the concept, the easier it's going to be to do the multiplicity of trades around the table, CN, CP, Feds, Prov, municipalities, regions, VIA, Metrolinx...and private investors.
I agree with MD, stick to the basics for now, and that will be twin track most of the distance, albeit highly signalled and hopefully PTC. And with the present hydro towers staying intact. Dedicated passenger can be added later ostensibly when some/all of those hydro lines are buried, and release a lot more width in the corridor.
This concept has to be as simple as possible to sell it. And a twin common carrier does it. If need be, a third track lay-by can be added where needed, but I don't see it being necessary if the line is signalled and dispatched efficiently.
Another point, a very important one to keep this as the basic original concept:
Since the Feds are needed not just for funding, but for the immense power of the Railway and the Railway Relocation and Crossing Acts (and a few lesser ones), the Fed powers won't pertain to doing more than is what is considered meeting the terms of those Acts...to the word! The Feds might have to get 'heavy' (walk quietly, and carry a big stick) to make things happen, they're not going to squander that effort and risk nasty court cases to do the job of the province. The Acts pertain only to the basic by-pass as envisaged. And that, initially at least, is freight. Once that's done, then secondary plans can be discussed. The hard part is going to be knocking heads together with the threat of the big stick to make them all sit at the same table and talk, then barter. "Arbitration" I believe it's called. No agreement by shared will? Then the Feds mandate the outcome. It shouldn't have to come to that, this is win-win-win for all concerned, and especially so for Johnny Plebe.