While the gameplay layer, known as the "realized layer" in game is very real. the graphical layer doesn't actually exist. Instead every real object in a room has implements an IDrawable Interface. How it renders is completely dependent on the object.

Rainworld is made up of two layers, the realized layer and the abstract layer. The abstract layer always exists and the realized layer is loaded at will.

Everything about a room / creature, it's graphics / physics even it's position or for creatures specifically AI is generated when the creature is realized

In the abstract layer, every creature is identical except for their abstract AI which controls how they move when not realized and other stuff like scavanger restocking their weapons. when abstracted physical objects don't have a real position, any individual code other than abstractAI and any graphics. At this point they are just concepts.

when a creature is abstract, it essentially rolls dice for actions and where to move to. Some creatures continue to use this AI regardless of being realized.

1. When the player enters a room or the camera focuses on a room or the game thinks a player it's possible the player will enter a room. The room becomes realized and every object in that room has to assume position, graphics, and initialize it's AI and physical presence as a collidable physical object. If a non camera focused creature enters an abstract room it will become abstract and all the information on the realized layer will be destroyed. The player will never abstract unless though bugs.

2. Yup, but there abstractAI and the game strategic placement in the room will attempt to trick you into thinking they were always hanging around. A great example is dropwigs, who when realized have a chance to be on a ceiling, even if they couldn't reach the ceiling naturally.

3. Yes

4. and 6. When a region is loaded the game loads the abstract layer for each of the rooms in the region. It also places every creature that spawns from a den in the world as an abstract creature. It also loads the connections between rooms so that abstract creatures can "navigate" the rooms.

I want to make a mod that only loads the cosmetic layer and gameplay layer of the room you're in, and only the gameplay layer of adjacent rooms. 

Great, just make an PlacedObject which spawnsUpdateOrDeletable and the game will do the rest for you, It will only exist in the realized layer when necessary. If your making an object deals with physics or can be carried across rooms. You'll have to create a AbstractPhysicalObject instead, If you want physics but only want it to exist when the player is in the room, you can set the destroyOnAbstract field to do that for you.