We build devices to investigate things based on what we believe we will find. So, it's hardly surprising that they tend to confirm our suspicions, is it? We believe in atoms and vacuums not so much because of Dalton and Einstein, as because of Epicurus, who planted that idea in our culture two thousand years ago.

I disagree. Epicurus had a theory that was in part, but not totally, discarded. However, other theories were completely discarded because they were found to be inaccurate. Dalton and Einstein devised theories based on evidence, and performed experiments; when they were right, their ideas remained, but when they were wrong, they were discarded. Photons and bosons have predictable behaviors, and to a large extent, they do not surprise us. In fact, we build endless technologies based upon what we understand about them. Of course there are probably unknown aspects of them, but what we do know is an advance of knowledge. It won't become untrue, it can only be better understood in a more complete paradigm.

I don't see 'what is known to be true' being overturned, but rather 'what is known to be true' is more completely defined. In so far as we began relying on evidence rather than thought alone.

As for wormholes and multiple universes, I do think such speculation is only that. There is no reason to believe that they exist, only conjecture as to how they might. Wormholes and multiple universes don't represent knowledge, IMO, just ideas.

That said, I do not believe in a 'true state' of the universe, but we have come a long way in establishing truths in interactions, which is the basis for anything knowable.