Metaphysical is a fun woo woo word, because one definition of it is basically as you have said, a synonym for supernatural (ie, physically impossible), whereas the other definition of it relates to metaphysics, the philosophical approaches to understand the rules that govern or give rise to the rules/laws of physics.

So you have one contextual usage that means 'weird unexplained spooky impossible nonsense', and another that means, 'logical structures that seek to explain the nature of reality as understood empirically, often by academics.'

Thus its a perfect word for mystical woo people who love to conflate different contextual meanings of words and pretend they are not doing that.