Hi Peter, sorry to reply late.
It's interesting because your use of 'metaphysical' corresponds to the new metaphysics of the 1960s with the rise of modal logic, in particular the formalizations and contributions of Kripke/Lewis. Their notions of metaphysical possibility and necessity concern fixing truth claims across possible worlds.
While these claims are not empirically testable, I can foresee a point where our computational modelling and simulation capabilities of ranges of natural phenomena will likely yield outcomes that rival empirical methods in accuracy. I guess these modal claims could in principle be testable this way by varying the relevant constraints, such as physical constants etc.
As for your nagging thought: I think that's perhaps the most interesting question in philosophy right now. Is emergence an anomalous phenomenon occurring at the cleavage of mind/body or is it a common phenomenon in nature across levels of organization. Both of these positions are difficult to justify, hence why a lot of philosophers deny the truth of emergence. This, however, raises the question, just what do we mean by emergence?
Without getting into the nitty gritty of a formal definition, my hunch is that there's no fundamental difference between the mind/body relationship and other levels of emergence, if they can be characterized as such. The reason I think this is that I don't buy into accounts of emergence that render emergent phenomena inexplicable by recourse to some 'physically' specifiable mechanism. As such, I'm committed to rehabilitating emergent claims within some naturalist framework.
To be clear, I think that emergent phenomena are emergent in that the new level instantiates novel causal powers not instantiated by its composing parts. But I am committed to finding a natural explanation as to how these emergent powers arise from combinations of lower level composing elements.
Therefore, to my mind, it's not enough to say that the neural substrate exhausts the causal powers of mentality, but that mentality resides in the complex organizational properties of the neural substrate, which is causally subsumed by the organizational closure of the living organism. That's a bit of rabbit whole of an argument.
But basically, the idea is that these novel causal powers sit somehow atop organizational variables. The same could be true for emergence at other levels of organization, such as, paradigmatically between life and non-life. The causal powers of living organisms are not found in their composing elements alone, but are instantiated by the organizational structure of the mechanism. Whether this is merely an innocuous rendering of emergence or whether there's something new here, is an empirical question worth investigating, including whether we can come with a general account of emergence that has explanatory power for purely physical phenomena.
I've answered that in so many words, but these are some thoughts in that direction. I would be interested in what you think as regards this question.