In the Burning Life and the "command section ejected" part, the ship in question was a frigate. Essentially, a heavy fighter designed for a crew you can count with your fingers. Larger ships would have command centers protected in the superstructure, with possibly some "bridge" or "conn tower" type structures. (For example, there's a clear window in the "deck" of the new Scorpion, right next to the rotating antenna.)
As for escape pods, technically you could RP that the capsule is some kind of an escape vehicle. However, that would also mean that if your pod is ever killed (as in, fighting another player), you're dead. Even that can be circumvented - don't update your clone, and you will wake up "with memory loss" from a backup clone taken the slow way a few days back. That could have some interesting effects, though I assume that RPing the memory loss would be quite a burden if you RP much, since you'd need to keep extensive notes on what all you have forgotten and should not reference. Even this might be circumvented by the character having a recording implant that gets periodically backed up (so after watching his sensations again, the memory loss would be at most hours), but that really starts to push the system around.
Not to count the fact that the pod allows you to command the ship the way you do. The pod allows you to learn skills while doing something else the same time. It'll be a lot easier to do things the "conformist" way. But how to be in a bar /sipping with friends when you're in a spaceship? Some bars have "holoprojectors", which you can remotely control. As attested in the Burning Life, these projections can be very realistic - kind of 210th century 3D graphics. Of course, you'll be limited on physical interaction, since it's just a projection, but with drone systems or hidden sensors and speakers, you can see, speak and listen - possibly even smell. Some places are assumed to be completely virtual, so it's all cyberspace, with simulated senses. Of course, you can also dock up and "be there" in person. If you're docked to another station, then you can assume that you've taken a personal shuttle from station to station, though this does limit you a bit. (In-station trade does not work, though contracts still work.)