Indeed. Say, maybe a civilization didn't start out with trying to build the world of particles of progressively finer size, but started directly with a model of fields, waves and charges and therefore never had a concept of a discrete elemental particle, and in turn a system built around that to categorize elements.

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".