Science makes no metaphysical claims but it is not unusual for scientists to make metaphysical claims, sometimes even in their scientific publications. That has confused the relationship between science and metaphysics. The philosophies of scientific realism and naturalism have further confused the relationship between science and metaphysics.
As a Christian I must say that if scientists make metaphysical claims, then their metaphysics should be consistent with Christian metaphysics. If scientists object to that, they should refrain from making metaphysical claims.
Science needs to begin without metaphysics. Mathematics has no metaphysics. So science should begin with mathematics. That is, mathematics should be the framework on which science is built.
Thus a science of space and time begins with a mathematical formalism. This formalism should be distinguished from the empirical units employed to measure space and time. As far as I know, that has not been done, so people have confused the measure of length with the form of space and the measure of duration with the form of time.
Isaac Newton separated his metaphysical claims about space and time into what he called scholia in his Principia. He should have just adopted a mathematical formalism and left out any metaphysical claims.
In order to distinguish the formal and material space and time, I have revised the Parallel Glossary for Classical Physics, see link above.