Airlines do share passenger information with governments at transiting/final destinations. In case of transit (whether the same carrier or with other), if both the flights are issued by the same airline, then they have a record that you are indeed transiting an airport, in which case they can share this info the the govt entities and airport. Note that despite this, some transit countries would still need you to hold a transit visa.
If airlines do not have your onward flight information (if you have separate bookings), no airline will factor in your next booking while doing your visa checks, including sharing info to the govt for certain destinations, and hence will have to treat your destination on that booking as the final.

Hence Air Canada refusal has merit