It's easy to imagine that another species might have never conceptualized electrons as little balls orbiting around a nucleus. They are neither balls nor are they flying in circles, those are simply abstractions we like because they appeal to the way we perceive reality. The way we conceptualize electrons leads to issues like the wave-particle duality, so it's likely just a local optimum we got stuck in. Another species might not even think of Electrons as being distinct entities, maybe they think of the electron field as one large ocean with some waves in it, or they subscribe to the single electron theory, or something we have never thought of and might never imagine from our perspective.
It is also very highly constrained by how _we_ observe the universe. Beings with different sensory/cognitive capacities could develop very different models.
> equivalences between apparently dissimilar modes of presentation
If there was some mathematical equivalence between their models and ours, which is already a leap to assume, there is still a question about whether the specific measure used would be translated to something equivalent to our object length measure in their model, which gets much stronger than just some equivalence assumption. And it’s even stronger to assume that this equivalence could just be inferred without any other information apart from the disk.
For some extra-solar civilization to examine the probe and its plaque intact, it will have to rendezvous with it in space. It seems to me to be the greater leap of faith to suppose this can be done without having knowledge that is isomorphic or equivalent to our formulation of orbital mechanics. Do you have any concrete ideas about how this might be so?
How could we ever be certain than another intelligence (whatever that means) would be capable of understanding the intended message? Unless of course we are already starting off with the major assumption that the only things that can be intelligent are things like us. I'm not even sure that intelligent has any meaning aside from denoting behavior "similar to us".
Or to them, an atom is as large an arbitrary macro structure as proteins are to us, and so they would never consider two empty circles with a single line to represent something so big and chaotic. Or maybe they had the crazy idea of building everything of vibrating strings!
Who knows what the abstractions and approximations would be when the foundation of it all isn't "getting hit on the head by an apple".