>Espee did use Freight train numbers in locomotive indicator boards,

Again, from the Book of Rules standpoint, these weren't "train numbers" but "schedule numbers" of regular trains. Route numbers are a transit thing for the traveling public's convenience.

When an extra train was created (by train order authority from the DS), the train was identified by the engine number preceded by "X" and followed by "E" or "W" (N or S for a north-south railroad). So if engine 4294 was assigned to an extra, it would identified as "X4294E" (or "W") in train orders --except its own running order-- with its indicators displaying "X4294". There was no need to display the E or W in the indicators because the train could move only in the direction specified, as in "Eng 4294 run extra Spence to Eaglet", which is [SP] eastbound. It would also display white flags/lights to tell the world that it was an extra train not listed in the timetable. And it would have to have other authority in order to be on the main track at both Spence and Eaglet. This has become the "from to but not at" of TWC.

>although they were 2nd or 3rd class trains,( inferior to passenger trains )

2nd and third class trains aren't inferior to "passenger trains" per se but "trains of superior class", in this case, first class trains. Passenger trains were almost always first class trains, but the reverse isn't true. First class trains weren't always passenger trains, and the consequences of assuming so could be deadly. This is the reason why it's forbidden by the Rules to determine a train's class by looking at its equipment and make-up. Superiorty between trains of the same class was determined by direction, and the superior direction was normally listed on the subdivision timetable schedule page and the special instructions for the division (superiority by direction could vary from division to division and subdivision to subdivision).

In other words, the Rules themselves didn't make any distinction between passenger and freight trains, just the various classes of trains. It was up to the individual divisions to assign a train it's class, and this was done in the subdivision's timetable page(s). In order to make a definitive determination, which is vital to your continued employement, not to mention the safety of others, you had to use your timetable, a train order(s) listing regular train engine numbers and extras running against you, and/or those indicator displays (or check the appropriate train register when permitted).

>and their freight train schedules were not published for public consumption.

The employees could care less about public timetables. The employee's timetable schedules were the law which determined your employment/unemployment, and if the public timetable disagreed with an employee's timetable, the public timetable was plain old wrong, no ifs, ands, buts, nor fors.