I think you might be over-analyzing the scene. This movie wasn't about the discovery per se. Had it been, it would have been an entirely different movie. This isn't a creature-feature. Indeed, you could cut that image out of the movie entirely without altering a single thematic or situational aspect of the movie. You can argue it's extraneous -- which I essentially did -- but you can also argue that it serves one purpose, and one purpose only: to validate the sacrifices made by the crew. And that's not a minor issue. The entire movie was about the journey, the hardships, the willingness of men and women to take risks in the service of something they personally perceived as greater than themselves...the quest for knowledge and the benefit of humanity. That's what the movie was about, after all. It wasn't a "Oh, we discovered aliens! Yippee us!" movie. The final alien was just a concession to the audience, a way for the filmmakers to send the viewers out of the theater (living room, whatever) feeling that while the ending was brutal, killing off the entire crew, it was, in some small way, a worthwhile sacrifice, at least from the perspective of these men and women. It didn't need to be thus. They could just have left everything unexplained, with the viewer free to decide if it was merely an exotic chemical reaction, or whether they were all hallucinating, or even whether or not anybody would ever discover what became of them. An ambiguous ending wouldn't have changed the basic thrust of the rest of the movie simply because the movie was never about the actual aliens. That said, I'm glad they gave us some minor closure. Everyone's dead, but at least they accomplished something in the process.
As for the design, well...it's actually a relatively sensible one. Creatures on earth, and in earth's waters, have developed like they have for a reason. Evolutionary advantages tend to create certain modalities. In this case, the cephalopod design certainly makes sense in the context of the environment. The real problem with fictions about aliens is that pretty much anything we can imagine tends to have Earthly analogues. Almost every single mythical creature in human history, for instance, was a variant of, or cobbled together from, real animals.
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