It has to do with how PCI assigns memory. Intel defined PCI with three independent address spaces, called Memory, I/O, and Configuration. The Configuration space is the one where cards expose their Vendor and Product IDs, and request memory windows in the Memory or I/O spaces. The bus controller checks each slot to see if there is Configuration data at boot time and then tells the cards where they may use Memory or I/O space and whether they can use interrupts.
Note, at boot time, so something like the Second Wave needs to be prepared then to request its memory, I/O, interrupts, etc... but that depends on which NuBus cards are being used. So it has to remember the resources required by the NuBus cards until the next boot when it can request those resources using Configuration data from the bus controller. And the power may have been lost before the next boot, so it needs battery backup for that.
