Interesting thoughts. Quite hard to measure but for instance would you charge a different rate for delays going to work or coming home. As aside why is one always delayed when you want to get home early?
Would you factor in those people who allegedly lost their jobs because of the Southern fiasco?
What about leisure travel would you have a different rate to business travel?.
Then there's the internal cost of delay attribution which is alleged-to require a large number of people to manage this might add more.
Although the delay minutes are known for every train you would have to guestimate the number of people on each delayed train to get the total cast.
But I'm sur it could be done.
I think it could actually be much simpler than that, as all that is needed is a very rough figure. It should be much simpler than the congestion on the roads, as you know roughly who is using the trains from the tickets bought, especially those on season tickets, whereas it is impossible to know who is using the roads at any one time and how they are faring. It always intrigues me how a figure for the costs of congestion on the roads is arrived at.