I read through the release notes, and I didn't see any mention of this issue at all. The fix must have been a EFI firmware update (my Mac did restart multiple times during the update, so this sounds plausible), but nothing is mentioned about this anywhere.
I saw the firmware-update progress bar (one of several similar progress bars that macOS/OS X can show during startup) during a 10.12.2 update. So that's a bit more confirmation...