You have a replacement philosophy, not a separation between a philosophy and an empirical standard.
People who look to science as the ultimate authority do so from a philosophical POV. The decision that naturalism is the ultimate authority is a philosophical one, not an empirical one. You should learn the difference between the two.
You should also learn the difference between methodological naturalism and philosophical naturalism. People who look to science as the ultimate arbiter of truth do so through philosophical naturalism, not methodological naturalism. They also prefer to conflate the two and that is a philosophical decision, not an empirical one.
What I am talking about is adhering to methodological naturalism, because metaphysical naturalism doesn't make sense (claiming that which your system can't detect doesn't exist, argument from ignorance).
Science also has no business defining "truth." The guilty here exist on both sides. On one hand you have people such as Dawkins trying to say science gives truth, and on the other hand you have religious people who think science threatens their religion as an alternate truth. Such people are creating a problem where one doesn't really need to exist.