I agree with some of what you said, as I myself agree with the statement that there are objective truths and entities about the world that exist outside of human observation (mathematics, logic, etc.). Plato of course already made this observation 2,400 years ago, as he differed from Aristotle on this topic.

Almost every atheist I've spoken to is some form of relativist, naturalist, materialist (I initially was as well) - so the primary points that are raised to point out the absurdity of these positions is the coherence and uniformity of nature, the transsubjectivity of human knowledge, the adequacy of reason to draw conclusions from observation-- these are founded in absolute truth; if they aren't, they are no more than unverifiable probabilities.

Since you actually agree in the absolute truth of objective metaphysical principles then I will admit that I had unintentionally strawmanned your position, as you have now stated the universality of mathematical principles (the principles themselves are not empirically proven - only expressed) that are not material and exist outside of human interaction with them.

With your acknowledgement of the rational coherence and uniformity of the universe, with objective metaphysical absolutes - how would it logically follow that these principles and entities came from chemical matter and evolutionary flux?