I do get your point regarding cost, fuel savings and operational significance. I am not denying that.
My only point is - These ghat areas are pretty much the only pristine forests left in South India. All the plains have long been ecologically destroyed by humans. So, even if it is inconvenient in terms of time of travel, or being more expensive, further interference in these areas should be avoided as much as possible. Spending a couple of hours more in a train or saving a few lakhs of rupees in fuel costs are not such great problems that they require interfering with the last remaining pristine forests in the Southern part of the country.
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more... There are very few forests left in the east coast, and most of them are dry, scrub jungles and not lush tropical forests like the Western ghats. The Bandipur, Mudumalai and Nagarhole sanctuaries, despite being protected have been damaged excessively by the highways build through them over the years. The Western ghats are the only vast, true forests left here, and every possible step should be taken to make sure our presence there is as minimum as possible.