Rooftop beacons were for grade crossing safety. There were several different styles including strobe lights, but they were phased out in favor of ditch lights. I always thought that the rooftop flashers were better as you can see them from the side, ditch lights are only effective if you are already on the crossing. The point was highlighted one night when we were chasing an MRL train with all 567's for power headed from Yardley towards Hauser in run 8 after dark. There were still a couple of unsignaled crossings at the time and we noticed that coming up on them at a 90 degree angle after dark, the amber
flashers were all you could really see, you had to be right on the crossing to see the ditch lights (the units had both at the time).
xxx On BN there were a large number of units that had the amber flashers that couldn't be shut off, I talked with several engineers that complained that flashing light would catch the corner of their eyes and make them think something was on fire. In Pullman, WA the local power would idle near a couple of homes rented to college students who really didn't mind the engines idling, but would get annoyed with the flashing light all night and would frequently put coffee cans over the lights to block them.