Incase of beam stress diagram results of RSI, are the loaded case stress value inclusive of temperature stresses or should the stress of loaded and unloaded be added and checked with permissible value? 

Unloaded stage is a Construction stage 1 where only temperature is applied and resistance of ballast for unloaded condition is applied to all the sections.

While loaded stage is a construction stage 2 where further acceleration /braking and vertical load are added to structure and resistance of ballast for loaded condition is applied to location where train load is applied.

Loaded stage stress value is inclusive of temperature stresses and need not to be added to loaded case separately to check with permissible value.

Let's say we don't apply any further load (braking/vertical/acceleration) for loaded stage to verify that whether stresses obtained in unloaded due to temperature load are carried to loaded stage or not.

We observed same stresses were obtained in loaded and unloaded stage which verified that temperature stresses are added to loaded stage by midas itself which concludes that loaded stage are inclusive of temperature stresses.