What the Firmware Updater web page says, in big blue letter near the bottom, is:
Alt-F is running from flash memory, you have to reboot into a special mode before being able to flash.
the "FlashIt" button is disabled and a "SpecialReboot" button exists.
So, after hitting the "SpecialReboot" button, and after the reboot, if you again go to the Firmware Updater, the warning should have disappeared, and the FlashIt button should be enabled.
Isn't this what you observed? How could it be written in a more clear way?