That's because natural sciences are willing to look at historical evidence, and exptrapolate backwards in time. We call this process induction, and it is fundamental to all natural sciences, and almost all practical reasoning. Are you also down on astronomy and geology? What sciences ARE you going to allow us to keep? Crystal healing theory and crop circle theory?
All one has to do is listen to the stuff coming from Dawkins and some of the Dawkins type wannabees here or in any internet discussion to see this is so.
Dawkins, or anyone's, opinions on the subject of metaphysics are not part of the curriculum vitae of science.
The DIFFERENCE between the two statements you quoted above is that one of the two will admit that the naturalistic presuppositions...................
You should re-read what you wrote a little more critically--neither of the scientists you are invisioning have made intrasigent naturalistic shutout claims, just as would be the case with about 99+% of any scientists you might actually query. Scientists you might actually query, would point out that science makes no assumptions, good, bad or ugly, about indetectable metaphysical explanations. Science does claim that it is only about proximate physical causes for events, because that's all science is capable of, since science can only operate on detectable evidence, not indetectable evidence. Whatever the means by which you might investigate indetectable evidence, science does not have a negative, or positive opinion about it, science only knows that it isn't within science's sphere of competence.