No, it IS a metaphor. This is what we do- we take an understanding of ours and apply it at a different level. Like we think photons act like particles and waves. They don’t. It’s just that WE think in terms of particles and waves.
At every level, yes, each thing is comprised of parts, the things interact, and the things and their interaction make up a larger system. But at each level the rules are very different. In fact, whole separate “sciences” are created to study each level.
So yes, humans are to society like cells are to an organ. But how about humans to a family? To a community? To a city? To a culture? To a nation? To humanity? To the economy? To the arts? Our brains like to compare and recognize similarities.
I agree, we can learn a lot from these metaphors. And I agree, we’re not at the top. But humans aren’t cells. Plus, we don’t know what’s at the top. We barely recognize what’s happening at the next level, of family, community, culture, economy, etc.
And the interesting part is that atoms can’t consciously work together. Nor can cells. Humans can, and at times do, a bit. And we could create a system that allows us to do it much better. In fact, it could be done now, pretty inexpensively. What’d be possible then?