Dear Vinay,
You ask a number of questions, that, I believe, are all aimed at the same point, which is our comprehension of the 3-dimensional world we live in:
"So I would propose that a 'primitive notion' such as a Point is a fictitious entity that is somehow related to how the human brain makes sense of the world on a biological level.
Is it even possible to come to an understanding of the world without fictional cognitive categories? Could we somehow come to comprehend the world through its actual organizational structure, instead of comprehending it through human-made fictional categories as we are doing now? Can we really understand the world as it is, rather than in terms of its abstractions created by the human mind?
I have argued above that the fundamental building blocks of Geometry are fictional ideas born of the human mind. Are the fundamental objects just a creation of our mind to understand a seamless whole, owing to the cognitive limitation of the human mind?"
First, I would point out that one can watch very young children move blocks of various shapes in puzzles, and do so perfectly, long before they even have names for the pieces. So I don't think that they are operating on 'fictional categories' at all. I believe that they perceive ontological reality.
My essay Deciding on the nature of time and space treats this problem in a novel fashion. I hope you will read it and comment.
Best regards,
Edwin Eugene Klingman