They had done this change for Allp-DHN many years ago . Those days traffic was much lesser than what it is now. The train [13352] used to depart PER in its current time at 20:30 hours and have an early arrival at BZA around 5:30am also by skipping MAS.
Passenger associations then put pressure and then railways reverted back to getting the train halted at Chennai as PER was not well connected and amenities at that time was much lesser. I think they can rethink the decision and get more trains to skip MAS. It will save travel time to quite an extent.