There are actually two cases. The first case is that you never want some feature enable because of the motherboard design. The second is that you want some features enabled/disabled.
There are 3 pci slots on m758/m787. If I want to use all 3 slots, I need to disable audio/modem. However, some applications might not want to disable audio. Even storing IRQ assignment is also very useful for debugging purpose. Storing boot option is useful, too. I'm just thinking flexablity here.
-Andrew