You don't seem to get it. USB keyboards can switch to a PS/2 emulated device (that's what the BIOS setting does). This is for systems that don't have USB support. When the bootloader is loaded there is NO USB support because the kernel hasn't even been loaded yet.
There are some keyboards (both wired and wireless) that seem to get confused though, and this setting simply doesn't work. This is not a problem with the bootloader, or FreeBSD. This is an issue specific to the keyboard's firmware. Yes, keyboards have firmware, sometimes you can update it, most of the time not. Your keyboard (any keyboard actually) has a small microcontroller in it that scans the keys and sends the appropriate signals over the connection to the computer.