Lets say I want Scene A to be a ship interior with multiple player crew positions, and Scene B to be the ships playing field where multiple player ships (or player vs AI ships) with multiple camera views on each ship representing what a crew station would see (ie a gun sight view, a bridge window view etc), and then Scenes C1, C2, C3 being the User Interface for a crewman manning a Station on the ship (ie a Gunners Controls).
Can I have the players in Scene A control the movement of the ship and the cameras in Scene B?
Can I have players in Scene A walk to a console, man it and thus be transformed into Scene C1, and while in Scene C1 look at the appropriate camera view from Scene 1 on their GUI and use controls that effect Scene B (shooting guns turning ship etc) AND hear things or receive input from Scene A (other crewmen in the ship talking to them, damage to the ship, etc)?
Is it possible to have all those scenes running concurrently and interacting with each other in such a fashion?
When a scene is not loaded, it does not exist that objects therefore cannot be manipulated or changed. (=No. Data cannot interact between scenes)
Long answer:
Since unity removes all information in a scene when it unloads you cannot store any information of position or state of objects across scenes unless you tell unity not to destroy the object. But from your question it sounds like you don't want all the ships to be loaded in the new scene. When you for example see the control panel you only need the ships position. -not the graphics.
Unity has a method called DontDestroyOnLoad. But instead of calling it on all objects in all scenes and effectively merge every scene into one, it is possible to create one script that always exists in the game, no matter what scene is currently loaded. Within this script you could keep information on all ships, player positions and everything you need to keep track across scenes.
Every time an object is created in a new scene is could get the saved information in the "DontDestroyOnLoad"-script and update its position, rotation and what more you need to keep track of. And when a new scene is to be loaded (and the objects destroyed), you should store the information needed to recreate the object in the script.
This approach might take a while to implement, but i believe it's the best alternative to having all objects in one scene.