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"As many know, the Derelict Ship is of biomechanical origin, not electrical."

No one "knows" that. "Biomechanical" is a description of how something looks.  A fusion of mechanical and organic. It doesn't automatically mean the ship was a living thing. We don't even know if those wires are electrical anyway.  Even if you want to go the literal biomechanical route - why not call them capillaries?

@S.M

Just a thought S.M, just a thought.

Notice the absence of wires and ventilation tubing.

Ha ha wow thanks for sharing, Hammerpedes!, I haven't seen that scene in decades.

First off I love how the rover thingy sounds like an old ford pickup. And yes, the little bit we see of the Derelict interior is pretty sad. But don't read too much into it.

Cameron is good at some things and not so good at others, that's about all there is to it. The only hidden story here or across all 5 films is the retroactive attempt to make all the various director's visions dovetail into a coherent whole, and so far the fans have tried harder than the film makers. 

That's why I find the whole idea of canon to be somewhat moot, so much in these stories hinges on the unexplained and in some cases total disregard for what went before. Everyone wanted in on this and to put their own stamp on it and what you get is a mess that fans will actually settle for having all been a dream. And maybe you're on to something, it does seem the one way to solidify everything. 

Last, that Newt scream is incredibly annoying. She would have made a great egg.

"Notice the absence of wires and ventilation tubing."

Apart from the one right next to Dallas' head?

The wires are coming out of tubes in Aliens. So no reason they'd be visible here.

"so much in these stories hinges on the unexplained "

What hinges on the unexplained?

I may have to dig up the direct quote...

But i am sure Ridley had said the Derelict was Alive and HR Giger too.

But at the very least they are some Bio-Mechanical Technology where we cant tell which is Mechanics and which is Organic....  The Xenomorph was more Mechanical in some way.

The Derelict and Juggernaught do differ a bit, but Ridley did say one was in New Pristine Condition and one was Derelict but we could also be seeing different models too.

Thus the Derelict is...

Juggernaught is

As far as the Wires in Camerons Alien deleted scene.... i think maybe we should only consider the look of the 1979 Alien Derelict and 2012 Prometheus Juggernaught.

Why?  The scene is part of the film, and changes nothing about the Derelict.

I think as far as the wires, and how we dont see this in the other shots of the Derelict.... but thats not to rule out that behind it all they would use somekind of Wires.

I mean Androids have Wires etc dont they but they are not like traditional wires we use today and so yes, who knows... but its as you said SM

The shot of the wires is not relevant to any way we should view the Derelict, it does change nothing really.

We also have to assume the Xenomorph is maybe related someway to the ships Technology too, they have a lot in common... purely Coincidence ?

?

so we see the head has a lot of Mechanical Pipes etc going on and who knows if these contain wires?  But it would be safe to Assume the Derelict has also as much Mechanical parts to it and so why not have wires?

And they dont have to be Wires as in what we traditionally use today.

Ash had normal looking wiring.  And fibre-optics.

The Space Jockey and Chair shows us a very Mechanical Look too... the Chair and its Scope Apparatus have a more Mechanical look to them.

The Chair connects to the Space Jockey via what look like Wires and so yes why cant the ship have Wires?

Yes thats what i was talking about... not traditional wires... which i think the OP assumed the Derelict had the look of in that shot..

As above with C3PO

Ash his wires etc where not the same for the most part as the design of traditional wires, but this does not mean they dont have the same purpose.

And so my point was we can not assume the Derelict shot with Wires, means its Wires like in the C3P0 image.

But as the Xeno and Space Jockey Chair have a Mechanical look to parts of them, then we cant rule out they have some kind of internal wires that operate on a more advanced level and that are also not similar to traditional wires as we see in the C3P0 image.

The Space Jockey and Derelict were HR Giger designs and with his work its always where Flesh, Bone meet Machinery and Mechanics and with a lot of his work your not supposed to be able to work out where the Biological Elements Start and where the Mechanical End.

And as you said... a slight thing like these wires, does not really have to change anything as far as the Derelict etc.

S.M.-

Keep in mind I'm only commenting on what's depicted on screen:

Until recently the SJ was unexplained, and certain fans (myself included) maintain its still unexplained.

How an egg got aboard the Sulaco is unexplained.

The Engineer's intentions are unexplained.

The list goes on, some of it is intentional obfuscation to serve the mystery, some is questionable writing, and some is creative egos feeling they have more to offer than thise that went before. The above are elements that the stories hinge on.

@BigDave

I see your point! The big picture is the one that really matters, agreed!

@Aorta

Thank you! I agree that fans such as myself have given quite the convolution to the franchise. Best to keep to the plain truth, not confusing theories. And yes! Newt would've made a cute small egg!

@Aorta

Not sure what you mean by the stories hinging on these unexplained things. The Jockey doesn't need to be explained.

Nothing hinges on the Sulaco egg.  Yes it's unexplained, but there was a Queen on the Sulaco, eggs come from Queens. It didn't just appear out of nowhere.

Engineer motivations is a bit lazy - they shouldn't ask question they're not prepared to answer, or at least give us a hint - but if it gets explained in the next one, no harm done.

And yet without these items, there's no story. In Alien, no story as we know it, and have been debating/speculating about for 35 years. 

Without the egg aboard the Sulaco, everything is ok, no story.

In Prometheus, there are hints, and the writing is questionable but the spirit there does seem to be to carry the debate and speculation forward.

The story doesn't hinge on the Jockey. It hinges on a monster getting on the ship. The Jockey could've easily been omitted (and was for a while), and they just find an empty ship with eggs.

With Sulaco egg - the lack of explanation doesn't break the story. It, like aspects of Prometheus, are just a bit lazy.

SM- 

Whether or not the SJ is necessary isn't the point, the story we were told is that it had some kind of interaction with those eggs, in or near that location, where they were found by the Nostromo, which was awakened by a distress call originating from the Derelict, which houses the SJ. So for the movie Alien, no SJ, no story. 

Yes, these stories are very elastic at the writing stage, but we can ignore  Giler and Hill's interpretations, I think. Everyone else did.

With A3 the story hinges on a couple of improbabilities: That there is an egg at all, and that for some reason the creature bleeds on the floor, starting a fire, the first item obviously being more questionable than the second. But without the egg, and the subsequent fire, A3 as we know it would not have happened. Thus, the story hinges on these elements. 

Anyway, this is confusing the only point I was really trying to make, that I highly doubt there is a franchise-wide secret sub plot tying all this together.