I could be completely wrong, but imagine that your cockpit commander is no different from the animated landing gear. There are aspects to the ship that can be modified, outfitting, ship kits, paintjobs etc.. but you can't remove a multicannon from the ship, it's stuck to it. Your cockpit commander is the same. For your commander to get up, they would have to be two distinct assets - all the things that encompass the ship and all thing things that encompass your onfoot avatar. If there were a way to seamless attach/detach those two things when motioning to get up or sit down in your cockpit chair, that could be an interim solution to the problem, with the restrictions on having to be docked/landed before you are allowed to get up and walk around.
It is the thing that those who go on about Star Citizen talk about, and it's true, when flying your ship in Star Citizen, it is your on foot avatar in the ship. However, it wouldn't surprise me that the animation of sitting down doesn't do exactly what I just outlined above. It's just that that game goes further in allowing you to get up at any time, even when the ship is moving. This is what people think about when talking about interiors, however, it's also one of the banes of Star Citizen in regards to lag/de-sync and why you see some of the crazy bugs in that game, and there's no real solution for it yet - it's what everyone wants but its computationally problematic, especially when bringing internet connectivity/synchronization into the equation. Empyrion acts in the exact same way, there is a heirarchy - on foot, hover vessel/small vessel and capital ship. In Empyrion, you can be in your small vessel and dock into the capital vessel, then get out of your small vessel, whilst in the capital vessel, then walk to the bridge, sit down and then fly the capital vessel with all hover/small vessels that are docked. But you can't dock a smaller capital vessel to a larger capital vessel. There are three distinct layers of object containers with rules that govern what they can or cannot do.
The tricky part is that everything in the capital ship has to be securely docked, which is the game's way of syncing all of the assets together so that when you fly, everything flies correctly with you. Anyone who's played Empyrion would tell you what would happen if someone who's in the captain's chair of a capital vessel started to move while a small vessel isn't properly docked to the capital vessel and also if anyone else, on foot, who's in the capital vessel isn't sat down. Because they are not docked/synced the ship moves but they don't move with it and thus go flying out of the ship. CIG have tried to solve this, with limited success, but having a ship that is moving and objects contained within it also moving independently along with the momentum of the ship, is prone to issues, which is why most games just use the dock/sync method.
I'm totally open to correction of the above or more accurate explanations from whoever has a better technical grasp on what is going on than me (not difficult).