Toronto-bound here as well. I emailed PAL last week regarding custom-clearing for Manila-Toronto flight, and here's their response:
Dear Madam,
Thank you for your email. Please allow us to clarify that when the flight stops in Vancouver, all passengers will be required to deplane and clear Immigrations in Vancouver. After clearance, passengers will take the same aircraft to Toronto. For further inquiries, please call our Reservations office to be assisted.
Thank you,
Customer Relations
Reservations
Manila, Philippines (24 hours)
Tel : (632) 855-8888
When PAL launched Manila-Toronto flight Nov last year, twas supposed to be a non-stop flight, but I guess they changed it as there's now a 1.5hr stop in Vancouver. I was kinda haggling with my husband to go this route to avoid staying in HK but he'd want me to take Manila-HK-Toronto via Cathay Pacific and clear custom in Toronto, and not in Vancouver.
I will call PAL probably once I received my PPR to clarify things further, and I'll ask them if 1.5hrs is enough to clear things in Vancouver.