Train numbers vs Route numbers -- actually not so rare at all. In fact still common on transit lines; typical is a small number box on the dash for the train number and an overhead sign for the route. Many bus lines are similar - route on the overhead sign, and run (train) number on the dash. Passenger ops almost always use a train number at least for internal timetable purposes so I'm not surprised that SN would have had them. Freight would be a different story, but is sounds from the above like SN used the more or less standard X(loco number) format so those weren't really train numbers; they were extras. Not many railroads had freights (other than perhaps a "headliner" train like the Super C - remember it?) on the timetable along with passenger.