Is there some way to impart inertia (or acceleration if you will) from the ship's movement, including collisions, to a player avatar walking inside the ship? The accelerations are so incredibly high (like they are in Elite, to be fair) that maybe it would make multicrew gameplay impossible anyway. Still, would it in theory be possible for a person riding a space ship (inside the ship's physics grid) to feel the acceleration of the ship (which is in the larger scene's physics grid)?
No, because you can't "feel" such acceleration under normal circumstances anyway.
But don't take my word for it though; Ben's going to come theory-craft it for you. Be patient.