The location of the boot drive is unrelated to the installation of a firmware update. The firmware is installed on the logic board, not on the hard drive.
Somewhat recently Apple started storing the firmware on the hard drive (a partition?) for the update process. Incidentally this means you cannot upgrade your firmware while booted off a drive formatted APM. I don't know the full process, but it restarts and reads the firmware off your hard drive and pushes that to the firmware on the computer.
And as for backgrading your firmware... #1 "why?" and #2 "I doubt you'll be able to pull that off"
The reason it started the firmware install without warning is you had told it to download updates in the background, so the firmware update was downloaded and sitting on the hard drive waiting for a restart. Disable auto-download if you don't like surprises. And it's a very good thing you didn't try to interrupt the firmware update. That
rarely ends well.
