Bhopal Shatabdi: chalti hai ek dum hawa ke mafik, speed aisi ke ruka de traffic - Varun

I agree with you. Let me list down my reasoning.
1. Mangalore need connectivity to other towns of Karnataka. For this, route via Sakleshpura and Castle Rock should be available. SWR is not interested freeing up Sakleshpura route citing HMRDA. Castle Rock route has its own problems. SWR is not interested in running even one train from its area (Hubli, Belagavi, Bijapur, Ballari, etc) to Konkan railway stations. So, if SWR takes over Mangalore, it will be of no use to MAQ.
2. For carving out Mangalore division, 600 kms of lines....
more...

Without touching Konkan railway, it is not possible. Konkan railway bring their expertise trains in difficult terrain. Their team can find out ways to cancel HMRDA and running more trains.
3. SWR is known for servicing neighbours neglecting own area. So if SWR takes over MAQ, number of trains from MAQ to TVC and Chennai will not reduce. (Do we need 5 daily trains to TVC and Chennai, whereas just one and half train to Bangalore? These 1-1/2 trains are running with 6 different numbers confusing everyone). This will be projected as a problem for starting new intra state trains. If KR takes MAQ, you can expect some positive response.
4. KR does not have/ own any rolling stock (trains). So, till now, SR provide trains for MAQ to Madgaon and central railway provide trains for Madgaon to Mumbai sector. Both SR and CR exploit the opportunity and run trains to suit their destinations. SWR only provide peripheral help. If MAQ goes to KR, it can become a strong player in the area.
5. Similar neglected situation in Madurai to Coimbatore route. Inter division issues. No proper trains between these major cities. Earlier metre gauge trains to Rameshwaram not restored. Nagercoil/ Kanyakumari neglected and trains are run via circuitous route via Kerala to suit TVC and PGT division areas.
6. Grand old Quilon Mail not restored after gauge conversion. No connectivity from Punalur Sengottai area to TVC as well as Central and North Kerala. Madurai division plays a role.