Jefferson was born in Virginia Colony in 1743. How do you propose he was a natural born citizen of a country which didn’t exist until he was 33 years old?
But it did exist, as explained by Madison.
The Commonwealth of Virginia most certainly existed in 1743. Madison explained that just because the colonies threw off the rule of the king, and entered a status in which they became free States, did not throw them back into a state of nature with no laws and no relationships of people to each other and to the society.
Yes, they instituted a new constitution (in most cases, although in a couple of instances they didn't even do that, but continued to operate under the same colonial charter they had always had).
But it did not change the relationship of the people to each other, or the basic relationship of the people to the Commonwealth. They had been natural born members of the Commonwealth before, and becoming independent did not change that.
Jefferson had been a natural born member of the Commonwealth of Virginia before Independence, and he remained a natural born member of that same Commonwealth. The Commonwealth joined with others to form a greater union, and they defined members of the greater union (the United States) as the people who were members of any one State.
So if a person was a natural-born citizen of Virginia, upon the forming of the United States, he became a natural-born citizen of the United States by virtue of being a natural-born member of one of the States that comprised it.
This is an accurate understanding of the way the Founders and Framers understood and defined citizenship.