(Not the OP) We don't know ho;w the human mind works, or how "intuitions" or "inspiration" come about, but that's no reason to call them "metaphysics". Clearly, they are physical processes that somehow take place in the human brain.
The questions you ask in this comment are good questions, for which we have no good answers. That doesn't mean there's anything supernatural going on, or that anyone is assuming something supernatural is happening. We just don't know how human scientists come up with new hypotheses, that's all there is to it.
But it's not like there's some kind of principled way to do it. There's no formulae, no laws, where we can plug in some data and out pops a hypothesis ready for the testing. Maybe we will find how to define such laws or formulae at some point, but for now, all we got is some scientist waking up one day going "holy cow, that's it!". And then spending the next ten years trying to show that's what it really is.
The questions you ask in this comment are good questions, for which we have no good answers. That doesn't mean there's anything supernatural going on, or that anyone is assuming something supernatural is happening. We just don't know how human scientists come up with new hypotheses, that's all there is to it.
But it's not like there's some kind of principled way to do it. There's no formulae, no laws, where we can plug in some data and out pops a hypothesis ready for the testing. Maybe we will find how to define such laws or formulae at some point, but for now, all we got is some scientist waking up one day going "holy cow, that's it!". And then spending the next ten years trying to show that's what it really is.