Had an interesting experience at YYZ Friday morning. Long line-ups even at Exec checkin counter, transborder. Travelling AC to ORD on an AirMiles freebie, the res agent wouldn't take my Cdn+ number to put on the file. Seeing the line and then seeing the machines, I thought I'd take a flyer and decided to use a machine. They show you can use your Aeroplan card or the credit card you bought the ticket with. No picture of an Cdn+ card. You then have the choice of entering either the flight number or the rec locator.
I slipped my Cdn+ card into the slot, then entered the flight number. Voila, it worked. The boarding pass came out, and even had my Cdn+ number and the notation CP*E (which would be the same as AC*E for Elite). I proceeded to U.S. customs and immigration.
But you are correct in noting,I'llMissCP, that they will not recognize CP flight numbers.