Resolved - Just thought of updating this thread after driving the Superb for some time post service.
The gear box found to be defective and replaced. These gear boxes are not opened (or) serviced in India. Hence a new gear box has been fitted along with replacement of intercooler / radiator assembly.
After spending a lot, the car is performing well for the last 250 kilometers after service. The car is running like a brand new one....
The skoda service center at Bangalore, and Skoda India responded well to all my queries and resolved the issue with the best of their effort!
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vprasanna's post in Skoda superb I 2.5 TDI V6 gerbox problem with fault codes was marked as the answer