If the Designer is "God", so what?
Also science cannot be limited to some arbitrary set of rules:
In any case, as Thomas Kuhn pointed out, debate about methodological rules of science often forms part of the practice of science, especially during times when established paradigms are being challenged. Those who reject the "teach the controversy" model on the grounds that ID violates the current rules of scientific practice only beg the question. The present regime of methodological rules cannot prevent the controversy for the simple reason that those rules may themselves be one of the subjects of scientific controversy. page xxv of Darwinism, Design and Public Education
The 2004 Encyclopedia Britannica says science is “any system of knowledge that is concerned with the physical world and its phenomena and that entails unbiased observations and systematic experimentation. In general, a science involves a pursuit of knowledge covering general truths or the operations of fundamental laws.”
“A healthy science is a science that seeks the truth.”- Paul Nelson, Ph. D., philosophy of biology.
“Science is the search for the truth.”-Linus Pauling, winner of 2 Nobel prizes
“But science can only be created by those who are thoroughly imbued with the aspiration toward truth and understanding.” Albert Einstein
The truth need not be an absolute truth. Truth in the sense that Drs. Pauling, Einstein & Nelson are speaking is the reality in which we find ourselves. We exist. Science is to help us understand that existence and how it came to be.
As I like to say- science is our search for the truth, i.e. the reality, to our existence via our never-ending quest for knowledge.
And it just so happens that science was once used as a method for understanding "God"'s handy-work.
Which means that those who do so today can only be as scientifically literate as the great scientists who did so before them. I would think that would be a good thing.
So if the designer is "God", so what? If science is interested in reality it doesn't care.
No one is saying that science has to say something about "God". But we may be able to make some determinations if we observe, gather data and evidence.
Science without religion is lame; religion without science is blind.- Albert Einstein.