I wouldn't care about it conforming to empirical science, we're talking philosophy. As far as I care, the matter could be the result of consciousness (however you'd define it), but labels are still going to help. Do those software/hardware analogies have flaws? Yes, absolutely. Strict labels are one of them, which you can illustrate with a 256-bit (or, hell, go past binary and make it 17-based—technicallities don't matter) emulator on a 32-bit machine. It's hardware running software emulating other hardware that could run completely different software – one exceeding many of the original hardware's restrictions. Or is the software only the top thing running there? Or should we go by something more general and assume whatever software does on the original hardware is just software?
Here's how you can go funky: if the original hardware in that analogy is the physical matter, the human body would be the next step (software), which created hardware (emulator) like philosophy to emulate higher concepts (software running on the emulator).
Find the limits of labels and go from there. There's no reason to fight against something that's so goddamned convenient and versatile, even if there are strong associations to them.