A common misconception is that the timetable schedule actually applied to a certain train or another. As you have correctly pointed out, the schedules could be applied to any movement. The dispatcher could and would hang green signals on the head end of a freight train and run it as the first section of a streamlined passenger train if the said passenger train was running late. Easier than making it an extra in many cases. It was prudent to notify opposing trains of the first section's engine number, just to be safe. This could be done with a message rather than a train order ie: "First 21 has engine 9044" ....
A great book for those interesred in traditional train operations is "The Rights of Trains.." can't remember the author's name but he was a Chief Dispatcher on the Western Pacific. You might find a copy of the book at a used book store or on the internet. I read once that if the dispatcher wanted to run a motor car (track crew) as the 20th Century Limited, he could do so with a clearance and orders and putting a set of markers on the rear of the motor car. This is true.
I would suggest that the lack of white signals on the Farmington Branch and others in the waning years was probably due to the railroad's redefining the branches as Yard Limits. This was a common occurence in later years on many lines - train orders were no longer needed, easing the busy dispatcher's job, especially when only one train at a time was likely to be out on the branch and speed limits were low. I don't have a Rio Grande timetable handy, but would guess that was the case.
Skip Luke
former dispatcher, IC RR, White Pass & Yukon, and Burlington Northern. Engineer, GL RR.