If you're not going thru space, the latter part would make perfect sense. After all, you'd have to deal with inertia should you stop, so belting up is a wise decision.The limit is still true by default in the config, and there are reasons for that, but yes he added a way to make them larger than 16x16x16. Doing so might very well be laggy on SMP, also players will have to be locked in their seats during the time the ship is in motion.
Also, wonder what it'd take to go full-on System Shock with Minecraft. Not just the tech and cybernetics, but the psionic abilities, too. Kinda like Ars Magica, only there's a penalty for depleting your reserves of power, since they rely on your mind; depletion would likely lead to short-term exhaustion. (Yes, I'm a huge Looking Glass Studios fan, could ya tell?)