They almost certainly weren't on free passes (unless the Scottish region had its own rules, as noted above.) I think there was a 4-mile limit on a free residential pass, and beyond that I think that beyond that you paid 1/4 of the public season ticket price, so there would have been payments for all those journeys - apart from Senior Officers and other top brass.
It wasn't a case of "no revenue" on that train, it was simply that the traffic department had to deliver what the personnel people had agreed in contracts of employment to get people to work for the railway (at what were quite poor wages at the time.)