Right, science is supposed to be different from philosophy, including metaphysics. But my point was just that scientists are supposed to clarify issues and provide real answers that solve mysteries (at least about how things work, or how a nomic pattern emerged), not posit miracles.

I agree that the universe that corresponds strictly to a finished scientific theory will seem deeply mysterious because scientists don't address the "why" questions that speak to our intuitions. (I have an article on that coming out in a week or two.) So philosophers would still have some work to do to make sense of scientific models, or to build up a responsible worldview out of them.