Inflated distances are easier to implement and more clean.
Since ticket prices are usually calculated on the basis of distance slabs, it will become very complicated if they implement a separate fare structure for just the Konkan region alone. Also, not all routes with inflated distances have the same level of inflation. Depending on the construction costs, some routes have more inflation than the others. Calculating ticket fares will become needlessly complicated if separate fare structures are maintained for each of these sections.
...
more... Using inflated distances makes it more simple, as a single fare structure can be used on any given route, and even the route passes through multiple regions with inflated fares, the same basic fare structure can be used.