No idea, probably Railways thought what's the point of halting a train at small towns in middle of night.
In up direction towards Mangalore it passes at very convinient timings i.e. Evening towards MNI and KHED. Going to these places from Mumbai/Panvel takes less time in this train than Bus, so the halts at that time make sense.
The end result of this is 12620 has a non stop 200 Km run :P