Sounds like there's a part of the story missing here. Only allowing pax into the customs hall 40 minutes prior to departure sounds way too little time for some. And as a "new system," sounds like there is something definitely off here.

There have certainly been times when the customs hall is full, and so they do call in by flight or montior the flow of people. As a Nexus holder however, don't know too much about this, as I can get through even in these situations. I do know that if the hall is full, it can certainly take over 30 or 40 minutes in the line, not to mention, getting through security, etc. after. I think the times I have seen the customs line out the hall in the last few months, they haven't really been calling by flight, but just holding the next people in line outside when the hall is at capacity. I think they did call by flight number early in the year, after the December incident on DL.

Perhaps something was happening in YYZ in the morning morning, maybe peak travel times and lack of a full US CBP staff or something that was causing them to need flow control. Highly doubt this is a new system.