You are overthinking this.
There is Fantasy. Magic, fairies, dragons and such do not exist, yet the suspension of disbelief works without a special effort on the author's part.
There are alternate histories. Utopias. Children's books about impossible creatures and events. Crime stories about crimes that never happened. Fiction with characters that do not exist! All the author needs to do is posit his world, and the readers will make an honest attempt at following him from there. All any author does is say: "A dragon attacked the knight.", or: "John loved Joan.", and – BAM! – there they are! Does he explain the existence of the dragon (or John)? Most certainly not! Because that would make the reader exclaim: "But that is not true!"
Every fictional story is a lie. Hercule Poirot does not exist and every reader knows it. No murder was commited on the Orient Express and every reader knows it. Yet we follow Poirot solving the murder mystery with interest. How does this work? Very simply. The author just says that Poirot gets on a train and that a corpse was found. That is all. There is no attempt to fool the readers into believing these were real events and persons, because that is completely unnecessary. All the author does is tell the story in the same way that she would tell of real events. Or in other words:
All the author does is not explain how dragons did actually exist and why we missed them. Because that explanation would break the suspension of disbelief.
Sure, there are stories that work this way and explain how a secret reality exists inside our own. But these stories must not only make an effort, they must make an extra effort, and their explanations must have no holes, because all the while the reader reads the story he will consider, think, and test, that explanation and try to find how it must be impossible. This is a whole different kind of story, and if you want to write it, your execution must be flawless, or it will fail big.
If you just want to tell the story of how a steam-powered rocket reached the moon, you must not explain how and why we were wrong and missed the truth (as Tommy Myron suggested), because that will only be laughable. If you try to make up obvious fake science that will cause the whole suspension of disbelief to fail. If on the other hand you just write it as if it was the most commonplace thing on earth and does not need any explanation of the technical details, because every kid learns about steam-engine space travel in school, then even physicists will enjoy your tale and suspend their disbelief most willingly.
This is why Donald Duck works. Because there is no explanation as to how a community of talking ducks exists but we have not discovered it. It is the absence of an explanation that causes the suspension of disbelief.
There are different kinds of SF. Hard SF, in which science and technology are the topic, will become obsolete as reality disproves those ideas or overtakes fictional reality. But in much of SF the technology is just the romantic backdrop for action, romance, or social issues. In other words: the plausibility of the technology does not matter.
But setting can age, too. PVC had an appeal of modernity to people once, but it seems cheap and ugly to us. Or think of the mobile phone. In Star Trek the wrist communicators appeared as a cool thing that everyone thought would be great to have; today the constant noise of incoming messages is so oppressive to some, that leaving the mobile phone at home is a rare luxury. Or think of wilderness. While a medieval forest was a place where outlaws lurked and people got murdered, robbed and raped, for us today wilderness is a romantic ideal that we yearn for.
This means that certain aspects of Star Trek or medieval romances may mean different things to readers or viewers of then and now. How interpretation will change is not something we can predict. But it certainly will change.