With 3.9 (and 3.X etc) kickstart one can press the help-key instead of holding both mouse buttons to enter early boot menu, with default 3.1.4 kickstart you can not, it seems - so amiga mouse becomes a requirement, even when you wish to use usb mouse or serial port attached mouse.
The point is to set it _before_ you boot, at the Boot menu. If you have multiple boot partitions, some of which will do a double reboot due to Rom Updates/SetPatch. Of course I know you can do it in HDToolbox, but it's too late at that point.