This type of availability has a name that I have trouble remembering, but it is something like 'short-haul-stop-sale'. It has been going on for years and the only thing that surprised me was that I didn't think that Res3 was capable in doing this when it first arrived at AC. Basically the system is set up to allow people to buy through tickets on segments that are closed for short-hauls traffic as the flights that is blocked YYT-YYZ is probably the only one that connects to PHL.

There is another industry term called 'Bid-Price' which means that the revenue management system adjusts to get the highest price possible for a commodity that may be in short supply. In your case the fare that you are willing to pay for YYT-PHL is higher than what someone else is offering for just YYT-YYZ. Thus the system is willing to sell you the seat at that price versus the lower amount for the first sector only. If someone wants to purchase just YYT-YYZ on that flight then they have to trump the YYT-PHL fare by paying a Latitude fare. AC have had this in place for some years.

I was surprised to see this effect also in terms of I class on multi-segment bookings. In many examples there was I class available for AAA-BBB-CCC but in looking just at AAA-BBB and then BBB-CCC individually, there was no I class available.