Let's say you loaded a room in and the player interacted with several objects. Is it possible to utilize this on runtime to save the state of objects in that room? I could imagine advanced persistence between loads or even in between game sessions.

It's a little unclear on the extension page whether this is compile-time only or if you can use the tools to pack in-game. Clarification would be appreciated!

Room file generation is compile-time.

If it's for game state saving/loading, I would suggest to look into variable_instance_ functions and saving into a buffer instead of JSON-based format. Depending on the game, you may want some custom logic on top (like handling surfaces/data structures, which are going to have different IDs upon load)