My statement was worded perhaps a bit too softly to make its point. IOW, it doesn't matter what is in the heart of the scientist or his intent. It is simply this - by not making a statement at all concerning metaphysics (e.g. the answer to question "A" lies beyond observation or measurement) - or by appealing to the anthropic principle (it just is) ... the scientist supports the metaphysical naturalist (atheist) worldview.
Albeit inadvertantly, such failures to clarify (or appeals to the anthropic principle) become fodder for metaphysical naturalist (such as on infidels) view of "reality" and thus their corresponding ideology.
To literally satisfy your objection, all scientific papers would require a disclaimer of metaphysical naturalism, lest the paper become grist for some atheist mill. ["I'm not claiming that God didn't cause this chemical reaction ..."] I think this is an unrealistic expectation. Science is what it is, not what some people might like to spin it.