That is exactly what I have been teling about Python rakes. They are not used for short runs. Python rakes are typically used for long stretches of 200-400 kms. And in addition do not jumble up the operations of a python rake with that of a passenger train with slip coaches. Both are completely different scenarios. A passenger train with extra coaches is still a single train. But a Python rake is essentially two 'separate' trains.
And no, there is no time wasted for a python rake in the yards. This is how it works.
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more... For example, consider 2 freight trains going from Jolarpet to Chennai, a distance of about 220 km. Now, JTJ is an interchange point between SWR and SR. So all freights enter the yard as they need to be inspected by the Directorate of Wagon interchange ( DWI). Basically, freight trains pool wagons from multiple railway zones to ensure maximum wagon utilization. So to ensure that no particular zone is being forced to pool more more wagons than the others or vice-versa, at zonal and sometimes divisional interchange points, freights are inspected, with the staff making a note of each zone's contribution in the rake, the health of the wagon etc. This can take anywhere from 2-4 hours for a fully loaded freight train depending on the number of freights in the yard and the traffic on the mainline. This is a mandatory halt time and it cannot be avoided.
Now in case of our example at JTJ, a typical journey from JTJ to Chennai for a freight can take about 6-10 hours ( SR's average freight moving speed is about 23 kmph). And during the day time, there are two open slots between 11:30 - 13:20 and 14:00 - 16:45, which have very less passenger traffic from JTJ ( this does not include any freights already on the route and the traffic between AJJ-MAS and KPD-MAS). For the 2 freights which moved into JTJ at about 9 AM and 10 AM in the morning, the inspections would be complete by 11:30 AM and 12:30 AM respectively. Now, with both trains departing separately, they would only reach Chennai by evening or in the night, and they would require a crew change en-route if they get delayed. And in addition, there are multiple freights waiting in the JTJ yard which are bound to other destinations like BZA, RU, KPD-VM etc. So, since both freights have the same destination or they at least have a common route till Chennai, it saves a lot of time for both trains if they are coupled together and finish the journey as one rake.
So, the train starting at 11:30, may be delayed by one hour to start at 12:30, but instead of reaching at 6 PM or later, it will reach by 3:30 PM and in addition, the 11:30 slot may be used for another freight and the tracks can be utilized better instead of keeping them free. And the additional benefit is that two freight trains use the same slot to reach Chennai.
Now, even if one of the 2 freights has to proceed further from Chennai, it is no delayed due to the python rake formation. This is because, Korukkupet/Tondiarpet yard is the last yard in SR before the trains enter SCR and most trains get the wagon regulation checks done here.
All this works because freight trains are not like passenger trains. They have long halts at many stations, unlike passenger trains which have short 5 minute halts. Most of the times, we can see multiple freight trains being made to wait at the wayside stations. These freights usually halt for at least a couple of hours before leaving. It is quite simple to see that, when two trains are anyway being made to wait for 2 hours at a particular station, it would save time if both are coupled and leave together ( of course, only if the traffic on the route and the availability of loop lines at intermediate stations etc is also suitable) instead of making them leave separately and occupy two slots.
Sorry for the long answer. :)