By not going through KR it serves more of Goa than it would with KR, as there are plenty of trains via KR anyways. In case of netravati or TVC rajdhani diverting via KR had no affect on how much stations it served in Kerala, and since there was a huge time benefit, it made sense to do so via KR. Even then, there are trains in kerala that go via PUNE rather than KR to serve intermediate passengers in other state.