जिंदगी में शादी के अलावा ट्रेन में RAC ही एक ऐसी स्थिति है,जिसमें दो अजनबी साथ निभाने को मजबूर होते है। - Junaid

Maintaining list of Junction points for a particular junction is more consistent way. If there are N lines converging at junction, then there will be N adjacent junctions mentioned in its page. This data will never change and remains consistent(unless some other station between the station and nearest junction becomes a junction with new line construction).
Just like hop by hop routing concept in networking. Particular router will maintain address of adjacent routers to which it is connected. This will ensure consistency.
Moreover if we consider what you said. You say that Kota...
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lies on NDLS-BCT stretch. Some other person will come and say Kota lies on MTJ-BRC stretch. Some other will say MTJ-BCT and this goes on. This makes things ambiguous.
Instead of that, taking smallest unique stretch like RMA-Kota, Kota-SWM, SWM-Bayana, Bayana-BTE, BTE-MTJ etc. will ensure more consistency and less ambiguity.
So it is better to take stretch between 2 junctions as an unique line rather than taking a long stretch having many junctions lying on it.
Hope I was clear with my point.