Just my personal gut feeling but I always considered entering a seat the pivotal moment as to when the game considers me an outside element (ship) or an inside element (person).
At least the scaling of the outside panorama seems to change at that moment.
Since you always move, climb or slide this way or that it's not really in your face. But I imagine to notice the difference.
Or maybe my spacial vision is crap. That might play a part too...
Okay, let's run with that. You are in an idris that has just been hit by another idris's rail gun directly in line with the gladius you are sitting in waiting to launch. In order to perform the damage assessment to your gladius, it will need to determine the damage to the idris (space server). The idris will then determine the damage to the interior of the ship (ship server), but it will also need to determine if the round will continue on into your gladius (or will it be stopped in one of the higher decks). This means the damage needs to come back out into the space server, reduced by the appropriate amounts and applied to the gladius. Assuming it goes through your gladius (it's destroyed), then you also need to determine the damage the gladius does to the internal parts of the idris (idris server again) PLUS remaining damage done by the other shot as it exits the bottom of the hangar and does damage to the other side of the ship (more ship damage)
As you can see, this type of mechanism can get VERY complex very fast. If everything was on the idris server (including the gladius), then you will need time to transition from idris server to space server as you launch. This means even a few seconds where you have no idea if you are flying out to see 10 hornets lined up on the bow, or a clear area.
I can see what CR is trying to do, but I am just not sure they can pull it off in a real time FPS environment the way they want without causing themselves major issues. If this were a game like EVE, WoW, SWTOR, or any other other near real time (but not real time), then this would be easy...or at least easier. Unfortunately, with an FPS style game, ANY lag becomes problematic, and going from server 1, to server 2, back to server 1, etc is just begging for lag issues.
Oh and before everyone says this is an idris issue only, it also applies to someone with a galaxy, polaris, carrack, etc if those have to become "servers within servers" as they will have the same issues.