Newton was a scientist, regardless of his religious beliefs. He was a scientist because he employed empirical methodology and reasoning. He looked for natural causes rather than miracles. He assumed the regularity and consistency of natural phenomena.
Anyone doing this is doing science, regardless of beliefs. Science does not comment one way or the other on the existence of God.
I fail to see what point you are making.
The point is that if science says nothing one way or the other about the existence of God, then it isn't a violation of the rules of science to suggest that God created the universe, created its laws, created life on earth, etc. It isn't mandatory to speculate that God did all those things. It isn't necessary. But it isn't prohibited.
Yet we're told that it is prohibited. That the only scientifically permissable opinion is to assume that God had nothing whatsoever to do with the universe, its laws, life, etc.