I guess by 'via Kota is shortest' you're considering the SC-PAU-AK-INDB-Kota-JP route, the two sections of which (AK-KNW and KNW-INDB) are yet to have BG lines. Moreover, the route although shortest as per distance, will be too slow owing to single non-electrified line.
NGP-ET-JHS proves to be the first choice, but already has more than enough services and is getting saturated.
The route chosen in contrast with the above is a new section, hopefully to open by the beginning of 2018.