It's sort of funny that the NSA can remotely flash a running system's hard drive firmware, but Seagate makes me make a DOS bootdisk to do it. they really do have tech that the rest of us can't conceive of.
They don't want to worry about your "reg cleaner" and ask.com toolbar suddenly taking 100% of the CPU and screwing up the firmware write.
Heck, BIOS updates are done the same way, pretty much. The Windows installer shoves the new firmware binary into a space the BIOS can access, reboots the computer, updates during POST/BIOS, and then only when its successful, reboots again into Windows. Its not run when Windows is running. You'd have to be a little crazy to do that.