What is the standard solution for preserving level data?

I've found different answers to how you might preserve data on gameobjects without resetting it when loading a new scene, such as DontDestroyOnLoad, PlayerPrefs, LoadLevelAdditive or even just using different positions in the same scene, but what is the standard solution commonly used in single player RPG games in the style of Pillars of Eternity, Neverwinter Nights and others, where the player character travels around many different areas (towns, dungeons, woods, houses) and upon returning to any previously visited area will find everything the way it was left - the dead still dead with the bodies in the same place, the living still living, the items picked up no longer there, the items left behind still waiting, things broken still broken, switches flipped the same way and so on?

Adding it up to a huge list of manually created variables seems not elegant at all. Is there maybe an asset for this purpose anyone could recommend?