I have run into less serious but similar problems with buses not getting the word about street closures. The way I (think) I have solved this is to keep digging with the authorities until I get an actual name and cell phone number of the bus dispatcher or duty officer who is scheduled to be on the job while the race is in progress. I have a conversation in advance of race day about the fact that any change to the modified bus schedule for race day could create a problem. I ask for reassurances that the buses will stay away from the course, and I get them. I email them a course map with the times. Then, I call early race morning to confirm. Before I did this, the drivers never got the word despite we had a permit with all the local authorities in which all affected parties were dutifully notified. The buses reliably tried to drive onto the course until they were stopped by police before I took these steps.
To my way of thinking, either the train company agrees to not cross the race route or they don't. I feel it is not necessarily the train company's fault if they promise to stay away and then show up anyway. The reason is that it is the RD's job to do everything short of parking cars on the tracks downstream to ensure the train folks fulfill their promise. I have learned that taking someone's word is rarely enough. For a rail crossing, the RD should insist on something in writing. If there must be some quid pro quo for such a written agreement, the race should pony up. If there is a written contract and a train still interrupts the race, the race then has the opportunity to sue for entry fee refunds and expenses.
IMO if the rail company refuses this kind of agreement, it means there is a good chance a train will cross during the race - at least this is what the RD should assume. In this case, the course should be redesigned. Apart from a Boston - like disaster, there is no excuse for a train going through the middle of a race. Full stop.