At the risk of being redundant (as I wrote a similar post on the old forum), I think there may be the possibility of a flexible and rewarding compromise between these two styles of play.
For starters, (if it need be said) the basic star wars/firefly adventuring model is at odds with the established 40k cannon. The Dark Millennium is simply too vast, too dangerous, and too terrifying to traverse without tremendous amounts of manpower and near-stellar energy. The idea of a small tramp freighter zipping around the Imperium is about as practical as getting together with four of your closest mates, renting a Bass-Boat, and setting out on the high seas to seek fame and fortune. You will -in all likelihood- starve, drown, or be eaten by sharks. In any event, you won't make it very far.
That said, commanding a starship the size and complexity of an industrial city has its own set of storytelling pitfalls. As someone pointed out above, there has never been a very successful or entertaining Star Trek Game. The unimaginable (and often undefined) scale of the Imperium's Star Ships is designed more to produce a sense of supernatural awe and Gothic dread then it is to present a realistic picture of space travel. It is, in essence, a literary convention and an atmospheric flourish (one that I rather appreciate, in fact). 40k isn't really proper Science Fiction, after all. A nuts-and-bolts approach to 40k space travel might just detract from the literary magic of the setting's conventions. If we are to ask practical questions about 40k starships, we might as well begin by asking why the hell they're covered with gothic stone-work and festooned with bell-towers.
Rather, the 40k vessel is more like the Imperium itself -awe-inspiring, unspeakably ancient, and tragically symbolic of mankind's hubris. To command such a vessel would require a person of extraordinary managerial skill, political acumen, military training, technological knowledge, endless initiative, and profound willpower.
This is all well and good, but without significant storytelling license, it might end up playing more like sim-city-meets-battle fleet gothic, with the tired convention of having to justify why such an august personage as a starship captain has enough time on his hands and sufficient disregard for personal safety to attend every away mission required under his command.
One also has to justify why the hell the other players should have any interest in obeying the orders of the player who happens to be captain. Obeying a GM-controlled Inquisitor is one thing, obeying one of their own is another thing entirely. Not to mention, a rogue trader has VAST resources at his disposal, which would make the usual chasing after loot and new toys a pretty hollow and unrewarding experience. Alternatively, it would be hard to justify to the PC's why they wouldn't have access to any given set of toys.
I'm not saying this wouldn't be entertaining, but rather it would be a rather different style of play from the more prosaic -and rewarding- rags-to-riches tale that most gritty adventure RPG's try to tell.
On the other hand, one could imagine that a rogue trader fleet could be replete with all manner of sundry characters out to make their way in the universe. The 'rag-tag fugitive fleet' might arrive in-system and disgorge a veritable horde of small, intra-system vessels -be they prospectors, missionaries, profiteers, idealists, cultists, etc- while engaging in the larger agenda as established by the Fleet-commander...(these 'smaller' vessels would be fertile ground for 'nuts-and-bolts' style cataloguing) The big vessels themselves may have populations on a par with some cities, after all. Why shouldn't the 'citizens' of the fleet have their own small transports, gunboats, prospector-ships, and freighters with birthing booked aboard one of the larger vessels. Being that a Rogue Trader fleet is as much exploratory and mercantile as it is military, one would imagine it would lack some unity of purpose and possess a great diversity of motivation.
To borrow from the very oldest RPG conventions, we could understand the setting with the following conceptual framework: In essence the Rogue Trader fleet and whatever system it happens to inhabit at the time could be presented as, in effect, an enormous mobile campaign-setting. The capital ship of the fleet could be looked at as a 'home town' for the players. A place to recuperate, seek medical attention, politic, adventure, buy gear (weapons, starships, etc) and birth their vessel while in warp-transit. The other 'big' vessels of the fleet could be considered other 'towns'. One could picture a pious ecclesiarch vessel, a liberantine collegium vessel, a dank and mysterious mechanicum vessel, all of them moving with the fleet and under the command of its mighty rogue-trader, but each replete with their own machinations and agendas, agendas they are all to happy to drag the PC's into.
The system the fleet currently occupies could be considered the 'wilderness' where the majority of 'dungeons' and 'adventures' take place. Beyond the protective arms of the fleet, anything is possible and the PC's are either free to do what they wish or to accomplish whatever missions have been set out for them by their masters (if they obey any masters). And if the fleet goes to war, its safe to say all aboard would be dragged into it in one way or another. The onus is on the players to make it back to the fleet before it transits out of system lest they be stranded forever, unless they are important enough to keep the fleet at anchor until they return.
This allows for a logical progression in power and influence, as the PC's move up in importance within the fleet. They might one day, if they live long enough, command a vessel of their own with a charter from the High Lords themselves. Or perhaps they'll simply get filthy rich and retire somewhere. The possibilities are endless, but do not immediately tie down the PC's with an enormous amount of narrative responsibility commensurate with a command billet. It also gives them a set of goals to strive for. There's always a better gun, a better starship, or a more prestigious posting over the next horizon. And if they want to command the fleet, that possibility is open to them as well, but they'll have to work together to achieve their goals. There is room within this framework for Inquisitors, Space Marine detachments, Pirates, cutthroat ganger-scum, mutants, Xenos, heretics, and all the other mortar and pestle of a good 40K tale, including a beat-up tramp freighter with a few extra horses under the hood and a few 'special' modifications.
It also gives the GM the option of constantly reinventing the campaign to avoid ennui. Perhaps the players get tired of the decade-long war of attrition with the inhabitants of planet-X, or searching out the terrifying ruins of planet so-and-so. After a suitably dramatic finish, the GM can simply declare that the fleet is moving onward to an entirely new system, new narrative landscape, and new set of missions or opportunities.
Wow, that was a long post. I apologize.