I've come across situations like this many times during my career.
The reason the FRA "suggests" that industries use the Blue Flag Rule to protect their own employees is that FRA authority does not extend to private trackage. So the FRA cannot mandate that private businesses use the Blue Flag Rule. But it is an excellent safety rule, and no doubt has saved many lives on both industry and railroad-owned track.
In my own experience as a Conductor and as an Operations Manager, I've witnessed more than a few acts of startling stupidity committed by customers on their own tracks. I've received orders to pull loaded grain cars from elevators when grain inspectors were still walking atop the cars. I've seen an elevator assistant manager set handbrakes on free-rolling cars by standing between the rails in front of the rolling cars, and hopping up on the end of the cars.
As long as this type of behavior does not impact my train crews, I would not turn anybody in to their boss. It isn't my or the railroad's business. I do have an obligation to try to prevent individuals from getting killed, even if by their own stupidity. So if I witness this stuff, I'll talk to the individual and try to convince them not to do this (and why). If I see a massive disregard for personal safety, then maybe I'd go to the supervisor.
I've also offered (when I've had the authority to do so) to give a short seminar on safe behavior around rail equipment, but never had any takers.
If your supervisor was willing to cut corners on safety rule compliance in order to expedite production (or for any other reason) he is at fault, and could be held responsible for injuries or death resulting from it. If you go along with it, you own a share of the consequences, too.
In matters of safety. either the Conductor or the Engineer can nix a move. I've only had to do this once. I was a conductor on a train that served a number of grain elevators. One of the elevators shipped corn to another one on the same line. They were both owned by the same company.
The crew of the shipping elevator thought up a sick "joke" to pull on the crew at the receiving elevator. They would find the grossest thing available and tie it to the end of a loaded covered hopper next to the brake wheel. This started out with items of garbage, and escalated to dead animals.
The last straw was a dead possum. I left the car and told my boss why. I told him I didn't think it was right to require me or anyone else on my crew to have to put up with this, especially considering the car was carrying a food product. My boss made a call to some higher-up in the elevator company, and the problem went away.
Do you have a Safety Committee at work? It might be good to suggest to your boss that your plant adapt Blue Flag protection for your fellow employees. I'd bet that even the railroad or someone from the UTU would be willing to give a short talk and question-and-answer session about how this works. If they won't do this, try contacting the FRA or AAR for assistance. I really don't think any of these groups would turn you down for a request to help make your workplace safer.
Ultimately, you are responsible for your own safety. I think fall protection comes under the authority of OSHA or your State Industrial Safety Department. This is a fairly new concept for grain elevators, when I started railroading, fall safety meant just not falling off.
You need to be aware, too, that railroad operating employees are forbidden to climb on top of railroad cars. Certain classes of non-operating employees are allowed to do this for specific duties. For example, carmen are allowed to to inspect and repair roofs of cars. Clerical employees are allowed to in order to check and record seal numbers, or at least could when I worked in that craft.
Les