Yes agree to this. Its only after coming of KR that there are trains from MAO, Karmali and now even Sawantwadi (MH). SWR was not able to do much for Goa state, I think under the garb of doubling difficualties in the Kulem-Londa route, they didnt prioritise much for Goa. And in a way people protests also gave weightage to their claims.
Fully agree with you that treatment to Mangalore by SR and to VSG/ Goa by SWR are almost same.
Such a small state like Goa gets torn between two zones is avoidable.
If KR gets MAQ from SR and VSG from SWR, things will definitely improve.