The first check is the mandated Doc Check to ensure you have proper ID and can enter Canada...

The second check as you board is to ensure that the Passport/ID actually makes it on to the plane with you (and isn't left behind for someone else or forgotten, which would deny you entry to Canada).

I was on a US Airways flight where we were stopped at the gate at YYZ for about a half hour while they determined that everyone on the plane had proper ID (1 person did not, for whatever reason, and was escorted directly from the plane). It's the airline's expense to take that person back where they belong...

That being said, you CAN fly to Canada on an expired Canadian passport - you just can't leave again until it's been renewed (as I found out once...)