macOS 10.12: MacBook Pro Retina takes hours (literally) to boot
It appears it was a hardware issue... I hope. Machine is currently with Apple having the logic board replaced. I recently discovered that the discrete GPU was not showing up under System Report, nor could gfxCardStatus detect or force it to be used. It seems my machine was one of the "very few" impacted by the nVidia chipset issue affecting machines from about 2011-2013, and apparently OS X is resilient enough that it just carries on in the face of soldered-on hardware suddenly disappearing, and doesn't consider that something worthy of bothering the user with.