I agree with you that a connecting track at Brampton (Owen Sound Sub to CN) doesn't really make sense. I would be curious what a fly-under and trenched section through downtown Brampton would cost. On the plus side, you'd be cut-and-covering, and could go under the CN corridor with a Verona system - making a weekend shutdown all that is needed. Not having to contend with OBRY rail traffic would mean unconstrained access to work, and not having to build bypass tracks around work areas. Much easier to work on a non-live corridor than a live one.