If you read the blog, it clearly mentions their method. I am quoting for your reference.
"However, our study has considered delays at all intermediate stoppages where passengers board the train as we believe that considering delays at all the stoppages is a more realistic measure and reflects the train traveler’s view about the delay on their train journey."
So to put it in simple words, the method was to collect Delay information for any Originating, Passing and Terminating trains. They just collected data from 2500 Stations throughout the country over a period...
more... of 6 Months. I think its a fairly reliable study and also their sample size (1 Million plus) is pretty huge and hence accurate.