I guess the biggest reason behind Running of trains to Chennai From Gujarat and Rajasthan via Navjeevan Route is that From Ahmedabad to Chennai the Route is totally Electrified whereas via Jodhpur-Ahmedabad-Vasai-Pune-Guntakal Route, It will have to go though the Route on a Diesel Loco, as Jodhpur to Ahmedabad and Pune to Guntakal are Still unelectrified.