I think this is a common misconception. Scientific theories provide predictive power, but they also provide explanatory power. The latter has fallen out of favour due to quantum mechanics, despite plenty of good interpretations of QM that provide good explanations, but it has always featured prominently every other scientific theory.

And given explanatory power is important, every scientific theory also therefore defines an ontology (your metaphysical concepts). This too has always been part of science.

> "String theory, loop quantum gravity, causal-set theory: these are just a few of the approaches that theorists have taken. ... But when you take a step back from the dispute, you notice all agree on one essential lesson: the space-time that we inhabit is a construction. It is not fundamental to nature, but emerges from a deeper level of reality."