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You ask a really deep question of whether an object is limited in its definition by what can be observed about it. You see to believe the contrary i.e. object is more than what it appears. But then, how would do you distinguish when all you have is observation to reason about? How do you tell if a given purple is of a Locastae or of the Pointakr if you've never seen either of them in your entire life?

You'll perhaps say Mathematics but you yourself admit that it's only the best we can do, and inherently has its limitations.

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It's not a deep question at all, which is wherein lies the fallacy.

We can and do add to our observations. Our vision is not 2D or 3D but "stereoscopic": we gain "depth" information by simply moving slightly, and we can move around a lot to get more info. Sometimes we figure out other ways to add more info, and sometimes we fully acknowledge that we can't do that and take the uncertainty as is.

This is all trivial stuff we do understand: we understand when we lack sufficient information to claim something with certainty.

Just like your example of square/circle/cylinder.

There are certainly limits to our understanding of the phenomena around us, but your examples miss the point, because they are exactly not it.