A BIOS on a IBM compatible (tm) PC used to work with PS2 port. Support for that was included in the BIOS and an old PC with an OLD BIOS will not recognise an USB keyboard.
This was a problem when poeople got the 'new' USB 1 based keyboards. An old keyboard was needed to enter the BIOS, the new one only worked after booting the OS (and with the OS the USB drivers).
Eventually (present time) we woeked around that by adding limited USB support to the BIOS. (Limited as in no support for most devices except for mouse and keyboards). This way you can use your keyboard before booting. When ther OS finally iunitialises its drivers it takes over from the old BIOS hooks.
Now we finally get to the problem. The USB3 controller is different from older USB1|2 controllers. Many BIOSses do not support it yet. (It will work fine from the OS once the OS boots and loads all drivers, including USB2 and USB3 drivers). But as long as you are in the BIOS you need to use the USB2 ports.
TL;DR; It should work:
- After the OS is loaded and takes over.
- And assuming there are no weird incompatibilities either from the USB3 implementation or because the keyboard integrated hub acts in a non-standard fashion.
Can you test the last by plugging the apple keyboard in another computer with a USB3 port?