Philosophy is limited in what it can show: a First Mover, an Uncaused Cause, a Designer. This does not prove the God of Revelation. For that you need Faith. Faith tells us that the First Mover, the Uncaused Cause etc. is God, that is the God of Abraham, Isaac and Jacob, the God of the Scriptures and Christianity.
The scientific method, and indeed science itself, is merely an artificial construct of man. But it is not an arbitrarily designed tool; it has been crafted to do a job. Namely, to aid man in understanding the natural existence around him. To subject God to this tool is to ask man to define Him by virtue of what is not included in nature. Therefore, if this is the measure of God, then whenever something is at last understood it is another piece of God that is taken from Him. I don't like that idea.
Philosophy is limited by what can be imagined, not by what can be shown. It provides sustenance for thought, and through thought, spiritual enlightenment. Within this realm man stands a chance at strengthening his grasp on God's true glory.
Science seeks facts, philosophy seeks truths. Facts require evidence, truths thrive on understanding. Which would you prefer to use to know your God?
You state: "To subject God to this tool is to ask man to define Him by virtue of what is not included in nature. Therefore, if this is the measure of God, then whenever something is at last understood it is another piece of God that is taken from Him. I don't like that idea."
I have not said the scientific method is the measure of God. Science is a tool that investigates nature in a determined fashion with tests using measurement and quantification.
The debate is about empirical observations of an order/design. Philosophers have argued that this order means that there is an Orderer responsible for the observed order. Christian revelation provides that this Orderer is the God of Abraham, Isaac and Jacob, the God of the Scriptures and Christianity.
St.Paul argues for this in Romans 1:Since the creaton of the world...God's eternal power and divinity have become visibile, RECOGNIZED THROUGH THE THINGS HE HAS MADE. (emphasis added) Romans 1:20
God is not subject to the tool. The tool reveals an order and design, which ultimately comes from the Creator.