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So I did some digging, and it's less clear than I thought.
I come from the embedded development world, where bare metal has been in use for a long time. Pre-2000s, this is exclusively what the term meant. Sometime around the mid 2000s, the virtualization services starting coopting the term.
So I guess it does indeed mean both, but being a stickler for tradition it doesn't sit right with me. The term just makes more sense when you're applying it to the hardware; bare. No middleman, and that includes an OS.