Wait so we're doing the whole "each service gets its own half of the ROW" thing like they're now going to do in the shared Stouffville/LSE corridor? That seems extremely silly...
It may sound that way, but I doubt it will be operated in that extreme a fashion, and I'm sure an awful lot of modelling will have been done by now to inform the design. And redone - the spec's probably changed as things like the East Harbour station were reworked thanks to the Ontario Line becoming part of the design.
When ML decided to abandon the planned flyunder at Scarborough Jct, and retain a "flat" junction, they accepted the need for one direction of the Stouffville line to cross somebody's LSE path. The least intrusive pattern is to have the two northernmost tracks carry the Stouffville traffic... probably interleaved with some part of the LSE traffic. Since the two southernmost tracks don't face any routing conflicts, it does make sense that they be through LSE tracks, likely carrying most of the express trains.
As headways are reduced with both LSE and Stouffville moving to 15 minute (or better) service, the fewer trains that need to cross over, the better.