Is it correct that I must take a train to Mughal Sarai Jn, or to Varanasi Jn?
It’s not clear what you mean when you say you “must” take a train to one or the other. A train to either one will get you to Varanasi. More trains from New Jalpaiguri stop at Mughal Sarai than at Varanasi Junction, and those that do stop there don’t run every day so you have more choices if you go to Mughal Sarai.. You can compare the schedules on the Indian Railways website at www.indianrail.gov.in If you click on “Trains between important stations” and fool around with it you can see which trains go to which stations and also compare the schedules of the various trains – total duration of the journey, how many stops, arrival and departure from each station — and also which classes are available on each train. According to the schedule, two of the trains that stop at Varanasi Jn also stop at Mughal Sarai anyway, but the other two don’t. I not sure it really makes a difference which station you stop at because one way or the other you’ll still be in Varanasi!