Especially at the beginning of a speculative story, all strange statements are taken literally. “Seed village” isn’t a metaphor, it’s what the village actually is.
I think of a story by Tom Maddox that appeared some years ago in OMNI. In the first or second paragraph he had passengers taken from their airplane to the terminal on what he called a “reptile bus.” I was teaching an SF literature course at the time, and my students were pretty evenly divided between those who had been reading SF for years and those who had never read it before that semester.
The majority of the experienced SF readers reported the same experience I had: At least for a moment, and often for quite a way into the story, we thought that Maddox wanted us to think that reptiles were somehow being used for airport transportation. We pictured a triceratops with a howdah perhaps, or an allosaurus towing a rickshaw. It was an absurd sort of technology, and it would have strained credulity—but many SF stories use such bizarre ideas and make them work. Maddox might have been establishing a work in which bioengineers had created many new species of very useful but stupid dinosaurs.
Those who had never read SF, however, were untroubled by such distraction. They knew at once that “reptile bus” was a metaphor—that it was a regular gas-burning bus with several sections so it snaked across the tarmac in a reptile-like way.
This is one of the key differences between the SF audience and any other. When confronted with a strange juxtaposition of familiar words, both groups say, “What does the author mean by this?” But the SF audience expects the term to be literal, to have a real extension within the world of the story, while the mainstream audience expects the term to be metaphorical, to express an attitude toward or give a new understanding of something that is part of the known world.
When an SF writer says, “She took heavy mechanical steps toward the door,” there is always the possibility that in fact her legs are machinery; the mainstream writer assumes this metaphorically expresses the manner of her walking and would regard that word usage as a grotesque joke if she did have artificial legs.
This doesn’t mean that you, as an SF writer, are forbidden to use metaphor. But it does mean that early in a story, when the rules of your created world are not yet fully explained, you should avoid metaphors that might be confusing to experienced SF readers. Later, when the rules are firmly established, your readers will know that terms that imply things that are not possible in your world should be taken metaphorically.
Recall the difference between metaphor, simile and analogy. Similes and analogies, which explicitly state that one thing is like another thing, are still available; only metaphors, which state that one thing is another thing, are forbidden. “You could treat Howard Merkle like dirt, and he’d still come fawning back to you, just like a whipped dog,” is a simile that would be perfectly clear and usable in speculative fiction, whereas the metaphor “Howard Merkle was a dog, always eager to please no matter how you treated him,” would be problematic early in a speculative fiction story because it could be taken literally.
Beware also of analogies that remove the reader from the milieu of the story and remind him of the present time. The sentence “The aliens had facial structures like eyebrows, only arched in an exaggerated way, so they walked around looking like a McDonald’s advertisement,” would be fine in a near-future story about contact with aliens; McDonald’s would presumably still be around. But the same description would be jarring if the story were set in a time and place so different from our own that the characters do not have McDonald’s restaurants as part of their daily experience. In that case, such a sentence is clearly the writer talking to the contemporary American reader, not the narrator creating the experience of another time and place. And it’s almost worse if you try to compensate for this dislocation by making it explicit: “The aliens’ eyebrows arched like the logo of that ancient fast-food restaurant, McDonald’s, which Pyotr had seen once in a history book about the 20th century on Earth.” This sort of thing throws the reader right out of the story. There’s a natural impulse to compare something strange to something that will be familiar to the reader—but as a general rule you should use only similes and analogies that would also be available to the characters in the story, so that the entire experience of reading contributes to the illusion of being in the story’s milieu.