Another thing to note...most times when you have an international itinerary AA won't let you do OLCI, you must check in at the airport with an agent to confirm your passport/visa details. So AA at ORD could issue you all the boarding passes but then as noted, you'll have to clear both Canadian and American immigration/customs and without NEXUS for fast track Canada entry and GE or NEXUS for fast track US entry, 50-minutes won't cut it.
As for AA letting you drop the YYZ-ORD segment and board your ORD-NRT flight there, they'd supposedly have to reissue and recalculate the fare on the ticket.