Chalukya is a rather odd case, probably due to it's slot sharing. SWR sure does some inexplicable things.
But there are quite a lot of trains for which SWR rejected an early morning arrival. Trains like Kondaveedu arrive in the late morning hours because of the same reasons. But this train might end up being diverted via YPR real soon. Even the additional slack might have been introduced keeping a possible diversion in mind. Most likely they are just trying to see passenger response to the train skipping YPR.