Science is indifferent to metaphysics. This is seen in the break between science and philosophy in the 19th century, and before that in the rejection of metaphysics by early scientists such as Newton. The scientific community doesn’t make metaphysical arguments.
The model science since classical times has been mathematics. The geometry of Euclid has been seen as the ideal for all the sciences. It is a model of conditional, systematic knowledge.
Euclid begins by considering definitions and axioms that are sufficiently simple and self-evident that everyone or almost everyone would easily accept them at least provisionally. Through logical argument and inference the reader is led step-by-step to see the derivation of propositions acceptable to common experience. Then new propositions are derived that are not obvious.
In the end a magnificent deductive system has been built that reflects inductive experience. But is it true? Not necessarily. The whole system is conditional on the truth of the definitions and axioms. Within science it is adopted as a convention. Whether or not it is true is not part of any science. (Whether metaphysics itself is a science is another matter.)
The history of science shows the indifference of science to metaphysics, though the success of science led many to accept it as metaphysically true. The most famous case is the geocentric-heliocentric controversy at the time of Galilei. Ptolemy had adopted geocentrism for his astronomy, whereas Copernicus had showed the advantages of heliocentrism. Galilei went beyond Copernicus and promoted a metaphysical heliocentrism, which led him into conflicts.
Geocentrism, heliocentrism, or the current astronomy with no universal center are all conventions that scientists are free to adopt for the purposes of science. Each has its advantages and disadvantages. Whether any of them represent reality is a metaphysical issue, not a scientific issue. Science is indifferent to such metaphysical questions.
TH Huxley famously said “Agnosticism is of the essence of science …”. He should have meant that science is indifferent, not necessarily agnostic. But he went on, “It simply means that a man shall not say he knows or believes that which he has no scientific grounds for professing to know or believe.” Tying science to belief or the lack of belief ties science to metaphysics. That was a mistake.
We all have our metaphysical notions but these should at most provide motivation for doing science or trying a particular line of research. Metaphysical commitments, no matter how much they are commonly accepted, are not part of science. Science is conditional.
Other posts on science and metaphysics are here, here, and here.