Thrash, if I could, I would tell it to Joss. The interior of his firefly is poorly laid out, for a Traveller based ship. I'm sure that the deckplans for the game are a close representation of the set designs, but that does not make them a good design. Almost 20% of the ship is taken up in corridors. There are a lot of extraneous corridors, double-backed catwalks and lots of wasted space, especially around the sick bay. This is of course my opinion. And locating the guest staterooms in the engine bulb makes as much sense as crew quarters in a warp naccel on the USS Enterprise.
When the firefly engages full burn, exterior vents, or fins, (what ever they are) open around the entire circumference of the engine bulb. It appears a fusion reaction blasts out of the slotted openings from inside the bulb, and is focused directly aft. If you look at the deck plan, the staterooms are within the fusion/reaction chamber itself. Form follows function (Sorry, I am an Architect after all), and the function of guest rooms do not belong in the form of the engine of any starship.
These guest rooms would be better located on deck two near the common room.
Don't get me wrong. I love firefly. I bought the CD's, and I can't wait to see the movie. We are going to get the game when it comes out as well. But since I'm and architect, I know a dumb layout when I see one. Changes would need to be made with converting a ship based on a TV show, to a ship based on a game that's been around since the seventies. I'm not so sure you understood my comments a critique. I intend to take the hull design of the firefly, and convert it into a Jump capable Traveller based ship.
Ok, deckplan aside, I do like your explanation of the turbo-fan. I never noticed the intakes closing upon breaking atmo. I'll have to look for it the next time I have the CD's in!

If converted for Traveller, it could be argued that they are in fact fuel scoops and fuel processors. When in atmo, instead of the processed fuel being fed into the fuel tanks, the fuel is immediately diverted to the reaction drive. This would allow a firefly class ship to "fly for free" in most atmospheres. If the ship is at rest, the fan blades could still drawing air (or water) into the fuel processors to top off the tanks. OOPS! Just saw the time, got to run.
JakNaz