I can understand that. As familiar as I am with Serenity, it still requires conscious effort of thought to place the cargo bay doors in the front of the ship, if only because I’m very much used to such being in the back (okay, stern and aft), and there’s not many shots in Firefly that unambiguously correct that perception.
I think you’re right and wrong about the arguments you’re presenting here.
When it costs $1000 (or more) per pound to orbit materials, you want to build the lightest possible ships you can, with the least wasted space.
But, it’s still true when dealing with less extreme economics.
I know that Cal Meachum has given a nice several discussions about the inappropriateness of using ships for speculative aircraft and spaceships. Nor do I disagree with his points. However, there are some factors that can be usefully extrapolated from naval architecture. And one of these is the fact that the most expensive thing aboard any space ship is going to be the concept of ‘open space.’
If one has ever been aboard any kind of large working ship it is always going to appear cramped, ugly, and small to untrained eyes. And this is on the surface of earth without the extreme costs of lifting material to orbit.
The reasons come down to several factors.
First, mass: Enclosing an open space simply takes up more construction material than eliminating that space would require. So, while the idea of a roomy rec room aboard a space ship doesn’t seem to be a mass-hog, the difference between building something that you or I would find luxurious vice something that were just barely adequate is going to involve increased construction costs in materials for construction. Increased operational costs in moving that increased mass of construction material to new destinations, and, here’s the key, no economic payoff for the owner for making that extravagent space in the first place.
Second, energy: Any kind of space ship is a finely balanced artificial environment existing in a hostile environment. That means to condition the air in such large spaces takes a continuing investment of energy - and the larger the volume of air to be conditioned the more energy it will take. So efforts will be made to reduce the load on the environmental plant. Again, not necessarily because the capability isn’t there, but because the economic payoff for such extravagence isn’t there.
There will be economies of scale coming into effect: As one’s lifesystem grows the per unit cost of conditioning and maintaining that lifesystem will drop. But the point at which the cost inscrease becomes negligible over the life of a given ship is going to be only for very, very, very large habitats, if at all.
Third, safety: False bulkheads, getting piping, electrical runs, and other such not-so-pretty things out of sight is a nice goal for people who have never had to live aboard ships. Most people I know who’ve had experience aboard ships, however, hate them with a passion. The reason is simple: a false bulkhead is a disaster waiting to happen. If a fire starts behind one, it is not unusual for such to beyond the point where it can be easily put out at the time of discovery. And for a spaceship, without the unlimited fresh air available to a waterborne ship, that’s even more of a risk than it is for current ships.
This makes a lot of sense. Given this logic, perhaps the dangling chains and open architecture of the Alien films is acceptable in a spaceship.
No open architecture on Star Trek TOS, then again there were no toilets on the Enterprise either… 
Fire at one with torpedos, the other with phasers. Plus, there’s always the copout that the USS Enterprise was a peaceful exploratory ship with an impressive weapons suite, rather than a battlecruiser in space. They COULD have put in more weapons (hell, the Enterprise E is bristling with torpedo launchers and phaser arrays in Star Trek: Nemesis) but for every extra torpedo launcher you are displacing potential sensor arrays, cargo bays, etc. that an exploratory ship would find more useful.
We’ve SEEN dedicated warships come from the Federation in the Star Trek series (the Defiant comes to mind) they tend to be small and compact, relying on agility and concentrated forward firepower rather than greater coverage like the bigger exploration ships such as the Enterprise and Excelsior. In fact, the Defiant is, at least in the general design concept, a Klingon Bird of Prey, but saucer shaped and with better armor.
Great topic. Well, obviously, Lexx is the most believable spaceship ever… Maybe not.
When the Wright brothers first got their motorized kite off the ground, I wonder if they envisioned a 300-ton airplane with eight bathrooms and a piano bar that could carry several hundred people halfway around the world non-stop? The Wright Flyer made the best use possible of the most advanced technology of the time (such as the more efficient gasoline engine the brothers had developed) just as the LEM, a van-sized craft with a hull of aluminum foil, did in its time. I fervently hope that in a few hundred years we’ll be tooling around in spaceships that would seem like fantasies to us now.