I don't deny that Newton was both Christian and a great scientist. I'm not sure what it is you're misunderstanding. If there's two doors to chose from, I'll do all the research I can before picking one. But if there really is a third door that I didn't see because science hadn't reached that point yet, then I don't include it in my research, even though all scientists after it will.
We had a similar discussion about Darwin in the Creationism debate. When Darwin wrote his theory it was still just a theory and very badly supported by evidence. When Einstein wrote his theory of relativity it was completely and utterly devoid of any proof. But later, both these theories where corroborated by experiments.
Newton made loads of research into the Bible. Numerology if I remember correctly. None of that has yet to be corroborated. I don't doubt for a second it was serious research. His religious theories haven't reached a point where there's any point in taking them seriously. Maybe at some point in the future we'll see some. But until then there's no point in believing in the Christian god is there?