The Scholastics developed a cosmology with the Earth at absolute rest in the center of moving concentric spheres. Ptolemy’s geocentric astronomy with its epicycles was thought to be consistent with the Scholastic cosmology. When geocentrism was challenged by the early scientists, the whole Scholastic cosmology was thought to be undermined.
The difference between science and metaphysics has been confused ever since.
For example, in his General Scholium to the Principia Newton wrote:
For whatever is not deduc’d from the phenomena, is to be called an hypothesis; and hypotheses, whether metaphysical or physical, whether of occult qualities or mechanical, have no place in experimental philosophy.
But then in his Scholium to the Definitions Newton goes on to give his opinions about absolute time, absolute space, and absolute motion. So much for staying away from metaphysics!
As the sciences progress they normally come to question their metaphysical assumptions, reduce the metaphysics, and become more formal and mathematical. Quantum mechanics as an example of science with minimal metaphysics. Some people think that is a problem but I see it as a success.
Philosopher of physics Tim Maudlin describes quantum mechanics this way:
Unlike Relativity, there is no agreement among physicists about how to understand quantum theory. Indeed, the very phrase “quantum theory” is a misnomer: there is no such theory. Rather there is a mathematical formalism and some (quite effective) rules of thumb about how to use the formalism to make certain sorts of predictions. … The philosopher of physics cares about the underlying reality and attends to the predictions only insofar as they can serve as evidence for which account of the underlying reality is correct.” p.xiii, Philosophy of Physics: Space and Time by Tim Maudlin
Like most in his field, Maudlin develops a metaphysics that doesn’t go beyond the bounds of naturalism. That’s his business but it’s not the business of science.
Other sciences are entwined with metaphysics. For example, the development of geology and biology as historical sciences conjured up first thousands, then millions, and then billions of years of time before recorded history. With no quantitative parsimony there was no cost for such magic.
The existence of time before the history of humanity is really about metaphysics, not science. What can be done in science is to show that the assumption of pre-historic time fits well – or not – with other science. Those with a methodology that includes quantitative parsimony (with or without qualitative parsimony) have an incentive to avoid such large metaphysical quantities.