.I'm also not fond of the idea that the Nostromo is essentially a hyperdrive module that gets attached to the refinery
My problem here is that as the very first absolutely irrefutable, canonical fact we ever get to learn in the movie is the caption that states “commercial towing vehicle ‘the Nostromo’”.
Somehow, this needs to be rationalised.
And as the ship is about the size of a gnat next to the payload she tows, it's hardly plausible that she'd physically tow the refinery. Ergo, she must do something else, "towing vehicle"-wise.
And if we postulate that a hyperdrive, especially one able to haul such a great mass/volume into hyperspace, is a very, very expensive piece of kit, then it makes sense that not every container or autonomous refinery barge is equipped with one.
And so it makes sense to me that the drive -- along with the systems to navigate it -- should only be attached to the payload for the journey, exactly the same way a present-day IRL plug-in deep sea ATB tug attaches a, for the tug's own size ridiculously over-dimensioned, propulsion to its payload for transoceanic voyages.
But it would hardly be economical to build such a specialised vehicle like a Swiss Army knife -- with lots of superfluous capacity for other tasks; able to do many things, but not terribly good at any of them. Nor could such a vehicle easily be retrofitted from some other kind of vehicle (at least from looking at IRL terrestrial examples).
Hence I conclude she must be built from the keel up around her single function -- the hyperdrive, and the systems to power, support and direct it. These must reasonably fill the bulk of the ship's volume.
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.But about it being too large. I believe this may be a screenshot of the Nostromo on LV426 or something close to it. Notice the little bit sticking out in front. That's the bridge.
That nose section does, indeed, house the bridge. But have a look at this image from the soundstage:
Note that the faceted viewport is the entire height of the deck, floor to ceiling - much higher than a man standing!
Using that as reference, you can see that the nose section alone could easily be three decks tall.
Then there is the shuttle. From the interior, you could surmise that the Narcissus must be at least ten meters wide (more like twelve from the scale of the studio models, actually).
But have a look at this image:
As you can see, the Narcissus is about 1/4 of the width of the "trench" between the main hull and the nacelle.
Reference that with this promotional image of the Nostromo model (not quite in its final iteration yet), where the "trench" is seen very clearly:
By that reference, the nose section could easily be 30 meters tall, if not more!
Further, there's the hyperdrive itself. If you look at this picture:
Those two bright, narrow slits in the centre are the engineering control room windows. This is what they look like from the other side (sorry for the blurry image):
Again, you can see that the space is at least an equivalent of a dozen decks high -- and this is in its entirety an interior space, somewhere inside the ship's hull!
The problem here is that the Nostromo doesn't actually add up. There is no single "master" model with all the detail in scale; there are numerous models and close-up models and close-close-up sets that depict various parts of the ship, and none of it will fit together. It's impossible to nail down an exact scale for the Nostromo. From different references, the end result can come out very, very differently.
Therefore, in doing what I have done with the deck plans and other work presented here, I've had to make compromises. It is obvious that Sir Ridley wanted to convey the size of ship that is truly vast, and I've gone with that.