Stoppage doesnt impact run-time, only if the train isnt high priority, as of Raj/Sha or the likes of high priority trains as like Tamilnadu, Karnataka etc!!
Swarna Jayanti do have the priority, which any normal SF do have & its not gonna overtake other SF on-route to cover its time lag but simply will follow them...
Stoppage simply are mostly for staff change, big junction etc & its as like other train plying the route!!