That’s true, if you have a lot of stuff in the world it’s going to be annoying. Though you might be able to do something like have everything outside the ship be parented to the same object, and simply rotate/translate that object with the inverse of your ship movement.
No idea if that really works, though. You might also consider using Scene2Ds or something for the windows instead, and doing all your movements on the sub-scene.
Alternatively, you could drive the ship the normal way, moving it, and just patch up the navmesh to be considered relative to the ship (if there isn’t already some functionality for that) so that it need not be updated every time the ship moves.
You should be able to make it so that stuff on the ship itself inherits the ship’s motion. Gravity is a different issue - you’d want to look into setting up custom gravity (there’s a thread, but no source, tho the OP of it offered to help others) such that everything in your ship gets a downward gravity relative to the ship, so that regardless if the ship is upside down to the world coordinate frame, gravity will be maintained as expected.
This stuff is very tricky, and something I’ve spent a fair amount of time wrestling with, though only in other engines. It’s not an easy problem to solve.