Dadar/Pathankot Express - ਤੇਰੇ ਬਿਨ ਮਰ ਜਾਣਾ

What is the logic behind Rail Traffic for IR ?
I am talking with regards to broad guage, double line traffic.
Is there a specific pattern that station masters follow to give a line clear to different trains? It is so uncertain regarding trains, sometimes a Superfast is stopped for a Mail/Express to pass; this affects the punctuality of the concerned train. Why some trains have to sacrifice their punctuality to maintain the others?
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illustrate, Sachkhand Express(12716) runs on time from NDLS, but after Agra Cantt. it is looped and Goa is made to run ahead of it, as if the authorities deliberately want to delay the timings of Sachkhand express. Goa and Sachkhand both are Superfast trains. How do they decide to move Goa ahead of it then?
May I know the logic behind this?