The above might be related to the "hub and spoke model" often associated with airlines. Instead of a direct journey, this way one books 2 or more tickets, gets off at an intermediate station, and changes trains. That's what "alternative routes" means above. So, something like "Board Mahanagari Express at Varanasi, get off at Itarsi, then board Karnataka Express to Bangalore".
The above model works very well with airlines, and in fact for international flights, one almost always changes flights at an intermediate airport.
The following concerns are there with trains:
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Train journeys usually last several days, whereas flights are for a few hours during the day time. In the case of train journeys, very often important junctions might come in the middle of the night. People might not want to get off a train at 2:30 am at night, and wait for their connection.
2. Very High Risk: Trains are very often late - so how much gap should be allowed between the two trains? Flights from airports depart every few hours - so even if a connecting flight is missed, one is put on the next flight in the next couple of hours or so. But, if a connecting train is lost, people might get stuck in a strange city for a long, long time. Tickets to trains have to be booked several weeks/months in advance - so even if the next connecting train is available, there is almost 0% chance of getting a reserved ticket in another train at short notice.
3. Cost: In the case of flights, a missed connection insurance is automatically provided by the airline - and it is the airline's responsibility to get you the next flight. With trains, it is your own responsibility. So, cancellation costs and rebooking costs are your own responsibility.
4. Luggage: Luggage movement between connecting flights are the airline's responsibility. But, with trains, the passengers themselves have to unload all the luggage and get on the next train.
For the above reasons, train travellers usually take just one direct train if possible. This site suggests nearby source and destination stations, for direct journey. When direct trains don't exist, in most cases passengers already know where to change trains, and they do 2 separate train searches.