Under the new system, my understanding is that pax transiting through YYZ enroute to SYD will have the upgrade advantage since YYZ-YVR-SYD are a single flight number and can presumably be upgraded at the YYZ-YVR check-in window, whereas pax connecting on other flights to SYD via YVR will need to wait until the YVR-SYD window opens up. This is an assumption on my part rather than a fact, and in practice it may not matter much considering the popularity of this route and the fact that most upgrades will continue to be handled at the gate.
SG